1. Trang chủ
  2. » Luận Văn - Báo Cáo

Báo cáo khoa học: Crystal structure of the tetrameric inositol 1-phosphate phosphatase (TM1415) from the hyperthermophile, Thermotoga maritima docx

9 268 0
Tài liệu đã được kiểm tra trùng lặp

Đang tải... (xem toàn văn)

THÔNG TIN TÀI LIỆU

Thông tin cơ bản

Định dạng
Số trang 9
Dung lượng 691,43 KB

Các công cụ chuyển đổi và chỉnh sửa cho tài liệu này

Nội dung

In the first crystal form, the tetrameric structure is symmetrical, with the active site loop in each subunit folded into a b-hairpin conformation.. The active site loop residues 22–42 co

Trang 1

phosphatase (TM1415) from the hyperthermophile,

Thermotoga maritima

Kimberly A Stieglitz1, Mary F Roberts1, Weizhong Li2and Boguslaw Stec2

1 Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA

2 The Burnham Institute for Medical Research, La Jolla, CA, USA

The extended inositol monophosphatase (IMPase)⁄

fructose-1,6-bisphosphatase (FBPase) family provides

an interesting case in which the changes in 3D

archi-tecture and structural flexibility can be linked to

increased specialization and emergence of new

func-tion This structural family was identified at the

begin-ning of the 1990s [1,2] Since then, the rapid progress

in genome sequencing has added many new members

At present, the family contains around 1000 sequences,

classified in three Pfam5 subfamilies, of which  600

are in the IMPase subfamily Despite having the same

architectural features at the single monomer level, the

proteins in this family show increasingly complex

oligomeric organization The inositol polyphosphate

1-phosphatases and 3¢-phosphoadenosine-5¢-phosphate

phosphatases are monomeric Most of the IMPases are

dimeric, although the Escherichia coli enzyme (also

known as SuhB) can be monomeric as well as dimeric

[3] All of the eukaryotic FBPases are tetrameric, and some are allosterically regulated by AMP [4] or oxida-tion of disulfides [5]

The IMPases in higher eukaryotes are involved in secondary messenger signaling by regenerating the myo-inositol pool, whereas the bacterial and archaeal counterparts may be involved in osmolyte synthesis, as has been postulated for the IMPase from

Thermoto-ga maritima (TM1415) [6] Members of this family show reactivity towards several substrates, including poly phosphorylated inositol species and

phosphorylat-ed nucleotides A few IMPase enzymes from hyper-thermophilic organisms also catalyze the hydrolysis of the 1-phosphate of FBP; these have specific FBPase, as well as IMPase, activities [7] We have previously solved two structures from this superfamily – Metha-nocaldoccocus jannashii IMPase (MJ0109) [7,8] and Archaeoglobus fulgidus IMPase (AF2372) [9] – and in

Keywords

fructose-1, 6-bisphosphatase; inositol

monophosphatase; protein folding;

thermophile; Thermotoga maritima

Correspondence

B Stec, The Burnham Institute, 10901 N.

Torrey Pines Road, La Jolla, CA 92037, USA

Fax: +1 858 7139948

Tel: +1 858 7955257

E-mail: bstec@burnham.org

(Received 15 December 2006, revised 5

March 2007, accepted 8 March 2007)

doi:10.1111/j.1742-4658.2007.05779.x

The structure of the first tetrameric inositol monophosphatase (IMPase) has been solved This enzyme, from the eubacterium Thermotoga maritima, similarly to its archaeal homologs exhibits dual specificity with both IMPase and fructose-1,6-bisphosphatase activities The tetrameric structure

of this unregulated enzyme is similar, in its quaternary assembly, to the allosterically regulated tetramer of fructose-1,6-bisphosphatase The individual dimers are similar to the human IMPase Additionally, the structures of two crystal forms of IMPase show significant differences In the first crystal form, the tetrameric structure is symmetrical, with the active site loop in each subunit folded into a b-hairpin conformation The second form is asymmetrical and shows an unusual structural change Two of the subunits have the active site loop folded into a b-hairpin structure, whereas in the remaining two subunits the same loop adopts an a-helical conformation

Abbreviations

AF2372, IMPase from Archaeoglobus fulgidus; FBPase, fructose-1,6-bisphosphatase; IMPase, inositol 1-phosphate phosphatase;

TM1415, IMPase from Thermotoga maritima; MJ0109, IMPase from Methanocaldococcus jannaschii.

Trang 2

this report we present the structure for TM1415, the

IMPase⁄ FBPase from T maritima

The proteins in the family share a common

mono-mer architecture and have common principles of

chem-ical reactivity A three metal ion-assisted catalytic

mechanism was proposed to function in the entire

fam-ily [8,10] It has also been suggested that the enzymes

might have a common origin in a postulated ancient

cyclitol phosphatase [7] One of the common elements

of this architecture is a loop that closes the active site

once the substrate binds Many of the eukaryotic

members of this family (including Homo sapiens

IMPase, inositol polyphosphate 1-phosphatase, and

FBPase) are inhibited by submillimolar concentrations

of lithium ions [11–13] Li+ therapy is an important

remedy against common mental disorders [14], and

inhibition of some of the human IMPase family

enzymes is believed to be responsible for these

thera-peutic effects We have proposed that the mobile loop

is the determinant of sensitivity to Li+[9]

In this report we provide an interesting addition to

this already intriguing protein family – the crystal

structure of an IMPase (from the hyperthermophile

T maritima) that has a tetrameric arrangement and is

also the most active IMPase known [6] Additionally, a

fragment of this IMPase (TM1415) shows unusual

structural duality The active site loop (residues 22–42)

comes into the direct lattice contact with itself In one

subunit it has an a helical conformation, whereas its

partner is in a b conformation Because this fragment

plays a crucial role in catalytic activity and may also

be involved in Li+ inhibition, the structural duality

supports the idea by Dunker & Wright [15,16], that

flexible protein fragments might be involved in

devel-oping new functionalities in proteins

Results and Discussion

Structure solution

TM1415 was expressed in E coli and purified as

des-cribed previously [6] The purified enzyme was

crystal-lized in two crystal forms, characterized by space

groups P21 and P212121 The structure was solved by

molecular replacement (molrep) [17] The structure of

both crystal forms showed a tetrameric arrangement of

this enzyme (Fig 1) More specifically, both crystal

forms contained a single tetramer in the asymmetric

unit The corresponding models were refined using cns

[18] at 2.2 and 2.4 A˚ resolution for forms 1 and 2,

respectively Refinement resulted in an R-factor of

0.209 and 0.178 (Rfree, 0.278 and 0.267) for forms 1

and 2, respectively (Table 1) Stereochemistry

meas-ures, such as the Ramachandran plot and backbone and side-chain statistics, were well within the expected values, as indicated by procheck [19] The electron density was very good throughout both models (sup-plementary Fig S1) with the exception of loop regions, and in particular two catalytic loops (22–42,60–72) on one side of the tetramer in the second crystal form The C-terminal region appeared to be much more mobile, as reflected by increased temperature factors The model for crystal form 1 contains the terminal Lys256, whereas the model for crystal form 2 was ter-minated at Gly254

The difference in electron density suggested the pres-ence of multiple water molecules, as well as a single

Mg2+in the active site of crystal form 1 (supplement-ary Fig S1) This metal ion is found in a classical octahedral coordination with Asp79, Glu65 side-chain carboxyls, the carbonyl of Ile81 and three water mole-cules as direct ligands In crystal form 2, the difference

in electron densities suggested the presence of a single tartaric acid molecule per active site The tetramer

of crystal form 1 is quite symmetrical, whereas the tetramer of crystal form 2 is highly asymmetrical (Table 2) The refined models of both forms contain

 300 water molecules

Monomer architecture: common family structure

As with other enzymes in this family, including FBPases, the protein has a well-preserved layered struc-ture of a and b secondary-strucstruc-ture elements (a-b-a-b-a) (Fig 1, left panels), falling into two domains The lower domain consists of a layer of two a-helices and

an extensive seven-stranded b-sheet containing the act-ive site The lower domain is reminiscent of the AMP-binding domain of eukaryotic FBPases (supplementary Fig S2) The active site is located at the bulge of the C-terminal end of the third strand with a characteristic DPXD motif, where both aspartates participate in metal ion binding The strand is followed by a two-turn a-helix that forms a phosphate-binding site The second domain has a three-layer motif with two layers

of a-helices flanking the second b-sheet This domain corresponds to the FBP-binding domain of FBPases The two helices of the first domain are connected by a mobile active site loop that previously was suggested

to modulate activity by co-ordinating the third metal ion needed for catalysis [8,10] This loop was also sug-gested to be involved in Li+inhibition [9] The average temperature factors for both domains oscillate below

40 A˚2, with helices being much more ordered than the connecting loops (See supplementary Fig S3 for the temperature factor profiles of both models.)

Trang 3

Dimer architecture: similarity to human IMPase

Despite being a bacterial enzyme and having

signifi-cant sequence divergence, the overall architecture of

the dimer is reminiscent of the human IMPase (Fig 1,

right panel) However, the dimer interface is quite

dif-ferent from the human enzyme and other nonarchaeal

IMPases The superposition of the second subunit of

the MJ0109 structure (1G0H) after superposition of

the first subunit requires a rotation of  15 along the

longest axis of the dimer in one direction, whereas

superposition onto the second subunit of the human

enzyme (1AWB) requires rotation of  15 in the

opposite direction The rotation around the axis that

intersects the self-contacting residue, Ile173, is denoted

as the dimer twist-angle To superpose the second

sub-unit on the structure of the eukaryotic FBPase takes a

30 rotation in the twist direction of the archaeal

enzyme In comparing the dimer orientation of all

these IMPases, we see that the human IMPase has the

extreme dimer twist-angle that is almost 45 off from

the dimer position in FBPases, whereas the TM1415 and MJ0109 constitute intermediate twists spaced 15 off each other (central panel of Fig 1)

Tetramer architecture: similarity to FBPase TM1415, besides being the most active IMPase ( 100-fold more active than its archaeal, bacterial or eukaryotic counterparts) [6], is also a very efficient FBPase [7] It is notable that the TM1415 structure represents a tetrameric organization for an IMPase (Fig 1) reminiscent of the eukaryotic FBPase organ-ization Each tetramer is organized as a dimer of dimers (Fig 1) Despite the fact that TM1415 lacks the additional helix (FBPases have three helices at the tetramer interface), the helical layers in both enzymes directly interact This dimer–dimer interface was shown to be crucial for the transition of the allosteric signal in pig kidney FBPase [20] The rotation around the axis that relates dimers is termed the tetramer twist-angle The TM1415 tetramer, despite having a

Fig 1 Schematic of the transformation of

TM1415 into the eukaryotic FBPase The

transformation requires  25 rotation of the

dimers around the tetramer axis and  30

rotation of the monomers in individual

dimers In the center there is a schematic

of the mutual relationship of the monomers,

in selected members of the family, as

indi-cated by the twist angle of the dimer.

TM1415 constitutes one of the

intermedi-ates between the human IMPase and

FBPase dimer organization In the

surround-ing panels, clockwise, startsurround-ing at the top

left, are the structure of the tetrameric

TM1415, the superposition of TM1415 with

the Homo sapiens (human) IMPase (in gold),

the superposition of Sus scrofa (pig) FBPase

with the MJ0109 (in blue), and the

tetramer-ic pig FBPase The secondary structure

ele-ments are marked in red (helices) and

yellow (b-sheets).

Trang 4

similar quaternary arrangement to eukaryotic FBPases,

is more twisted, and the lower dimer requires  25

rotation to superpose with the corresponding dimer of

the R-state FBPase It can be compared with an

over-rotated T state (the eukaryotic T state is over-rotated only 17 away from the R state, Fig 1) [21] As indicated in the central panel of Fig 1, a rotation of  25 in tetr-amer twist, and an additional dimer twist in both dimers of  30, are required to transform TM1415 into the FBPase

This nonregulated tetrameric organization of the

T maritima IMPase⁄ FBPase might represent an evolu-tionary intermediate between dimeric IMPases and the allosterically regulated tetrameric eukaryotic FBPases

As a reminder, not all eukaryotic FBPases are alloster-ically regulated by AMP (e.g chloroplast FBPase) [5] However, the quaternary structures of these IMPase and FBPases suggest that quaternary organization may

be critical in creating regulatory abilities

Crystal packing Both crystal forms of TM1415 have a tetramer present

in the asymmetric unit with similar packing of individ-ual tetramers However, in crystal form 2, the packing

is not as tight as in crystal form 1 In crystal form 1 (P21), the solvent content is 44.3% and the tetramers have multiple contacts with their neighbors Crystal packing contacts are numerous across the entire tetra-mer surface and include some weak contacts in the loop region (residues 22–42) The crystal contacts in form 1 leave sufficient room for unhindered packing of the loops in the b-hairpin conformation

In crystal form 2, the contacts are much more sparse, despite having almost the same solvent content (43.6%) as crystal form 1 Two important lattice

Fig 2 Schematic representation of the crystal packing in crystal form 2 Areas in contact are enclosed in the boxes Boxes in broken lines represent symmetry-related contacts to those enclosed by the solid boxes The contact on the left hand side comprises the active site loop (residues 22–42), shown in detail in Figs 3 and 4 At the other side of the tetramer, the active site loops are not in direct lattice contact, resulting in much higher temperature factors Both loops in the upper dimer, regardless of the packing contact, are in a helical conformation, whereas the lower dimer loops are in an extended conformation.

Fig 3 The view of the active site of both superposed TM1415

models (crystals forms 1 and 2) and that of human IMPase (PDB

code 1AWB) The model of the human enzyme (in light gray) has

three metal ions bound (yellow spheres) and the substrate ( D

-inosi-tol-1-phosphate, gray) The model of the TM1415 crystal form 1 is

in purple and the crystal form 2 in green (including the tartrate

molecule) The conformational change in loop 22–42 is indicated by

green arrows, and the change in the 60s loop harboring Glu65–66

directly co-ordinating metal ions, is shown in red arrows The

con-tact of the active site loop (22–42) in the helical (in green, crystal

form 2), as well as in the extended conformation (in purple, crystal

form 1), to the symmetry mate in extended conformation is marked

by a blue arrow.

Trang 5

contacts occur around the loop region (residues 22–42).

The loops on one side of the tetramer are in direct and

intimate lattice contact (two direct hydrogen bonds),

whereas the loops on the other side of the tetramer are

practically unhindered, without direct contact (Fig 2) Even though the crystal packing in both forms is dif-ferent, in form 2 there is still sufficient space around the loops so that the lattice could accommodate the tetramer with all loops in b-hairpin conformation,with-out significant structural changes (Fig 3)

Active site loops The direct comparison of both crystal forms provides unexpected insights into the principles of protein design and shows an unusual structural plasticity The tetramer in crystal form 1 (P21) is very symmetrical (the rmsds between individual subunits are listed in Table 2), whereas the tetramer in the crystal form 2 is very asymmetrical In the following discussion, we use the nomenclature suggested in Fig 4B, which identifies the upper and lower dimers in the tetrameric structure

In crystal form 2, the lower dimer has the active site loops in the b-hairpin conformation, whereas in the upper dimer the loops are folded into two short a-heli-ces (Figs 3 and 4) The color brackets in Fig 4 indicate the same fragment folded in different confor-mations in lower and upper dimers

Despite lacking any significant contacts, loops in the upper and lower dimers of crystal form 2 have distinct and different conformations (Fig 4) The loop (resi-dues 62–72) shows significantly changed architecture from a more extended conformation (b-sheet in form 1) to the more coiled conformation in form 2 The act-ive site loop (residues 22–42), and the loop (residues 62–72) in TM1415 are required for the formation of the active site in IMPase and FBPase [8,10] Figure 3 shows the superposition of both crystal forms of TM1415 and the human IMPase with a full comple-ment of metal ions and the substrate The structures superpose well at the active site region and the figure shows the change in conformations of those two active site loops (green and red arrows) Both loops harbor the residues involved in metal ion binding and there-fore the subunits with alternative loop conformation would be incapable of binding the full set of metal ions Additionally, residue Asp44, which plays a cru-cial role in the catalytic mechanism (creation of the nucleophile) in both upper subunits, has an alternative conformation in which it loses a direct contact to Thr84 Oc that is critical for water activation All of these conformational changes make the upper dimer catalytically incompetent

The catalytic loops in crystal form 1 have tempera-ture factors slightly higher than, but comparable with, the rest of the structure (Table 1) The stability of the loops is confirmed with the quality of the electron

A

B

Arg24B

α

β

Arg24B

Asp42B Asp42B

Lys31B Lys31B

Lys30C

Arg24C Arg24C

Lys30C

Fig 4 (A) The stereo-diagram of the active site loop (residues 22–

42) in contact with the same sequence symmetry-related fragment

(residues 22–42) covered with the sigma-weighted 2Fo-Fc electron

density, contoured at the 1.1 r level The helical (residues 22–42)

fragment (blue model) is covered with the purple map, whereas

the symmetry-related 22–42 fragment (purple model) is covered

with a yellow map The blue and red brackets denote the same

sequence in both models (B) Comparison of both crystal forms.

The crystal form 1 is in purple and the crystal form 2 is in green.

Please note significant displacement of residues 22–42 (loop 1) and

62–72 (loop 2) in the upper dimer The fragments enclosed in

boxes (with colors corresponding to the colors of the electron

den-sity maps in (A) are in contact in the crystal form 2, as presented

above.

Trang 6

density (Fig 4 and supplementary Fig S1) The

tem-perature factors for the loops in direct contact in

crys-tal form 2 (one in b- the second in a helical

conformation) are slightly higher than, but comparable

to, the rest of the structure; the remaining two loops have substantially higher temperature factors (supple-mentary Fig S4) and much weaker electron densities The symmetrical crystal form 1 has a single metal ion bound at the active site This metal contributes to the stabilization of active site architecture Choe et al [10] concluded that this particular metal ion-binding site is the most frequently occupied and has the highest affinity to metal ions in FBPase The metal ion does not make direct contact with either of the two mobile loops In crystal form 2, we found no metal ions, but

a single molecule of tartaric acid in the active site cav-ity This ligand does not interact with any elements of the active site loop Its location is somewhat reminis-cent of the sugar moiety of the substrate (Fig 3) Therefore, it would be difficult to argue that the tar-trate or the metal ion is the cause of the asymmetry The asymmetry must originate from two differently organized dimers present in solution that are dynamic-ally incorporated into the lattice during crystallization (supplementary Fig S5)

Evolutionary link The active site loop sequence (residues 22–42) is parti-ally similar to the human enzyme and partiparti-ally similar

to the sequences of M jannaschii and A fulgidus IMPases (Fig 5) In Fig 5 we present the alignment

of the TM1415 sequence with sequences resulting from the BLAST searches and clustering of all 786 inde-pendent sequences into 13 functional families Every sequence in Fig 5 represents a single protein family that has distinct functionality Figure 5 shows a small fragment of the alignment, including the mobile loop sequences Judging by the clustering of sequences, TM1415 is closer to the human IMPase The mobile loop sequence fits the environment less than other fragments (as measured by psqs, data not shown) The results of servers ranking this fragment propensity for order-disorder (disprot) [22] clearly suggest that this fragment has a tendency to be disordered There-fore, this fragment has evolved to be mobile and less structured

The characteristic element for our sequence is that, when aligned structurally with other members of the family, the fragment has low sequence conservation (Fig 5) It has variable length as well as amino acid content, suggesting that the fragment is rapidly evol-ving Even when crucial positions are preserved, differ-ent residues fulfill the same structural role (Figs 4 and 5) The other fragment (160s loop), predicted to be unstructured (supplementary Fig S4), participates in the assembly of the dimer and also of the tetramer As

Table 2 Comparison of the rmsds between different subunits

within individual crystal forms (off-diagonal terms), as well as

between corresponding subunits of both crystal forms (diagonal

terms) Please note the symmetry of crystal form 1 and asymmetry

of crystal form 2 represented by low and high values of the rmsd,

respectively.

Subunit a

Crystal form 2 (P2 1 2 1 2 1 )

Crystal form 1 (P2 1 ) A 0.931 0.739 3.937 3.335

a

The rmsds were calculated on the 252 Ca positions of individual

subunits.

Table 1 Data collection and refinement summary.

Crystal form

R merge 0.058 (0.41) 0.063 (0.55)

rmsd

Ramachandran plot (%)

Ligands and solvent

Temperature factors (A ˚ )

a Last shell data in parenthesis (2.2–2.27 A ˚ , crystal form 1; 2.4–

2.49 A ˚ , crystal form 2) b Loops in contact ⁄ loops not in contact.

Trang 7

presented above, the change in the aggregation state

contributed to a change in enzyme functionality The

inhibition, by Li+, of several members of the family,

must also be considered as an acquisition of a novel

functionality In summary, the low sequence

conserva-tion and high variability of both loops when linked to

their structural instability suggests evolution of novel

functionalities being driven by changes in sequence of

those fragments [15,16,23]

Experimental procedures

Cloning and protein production

The TM1415 protein was expressed in E coli, as described

previously [6] After cell lysis and removal of the cell

debris by centrifugation, the supernatant containing

TM1415 was heated to 85C and the denatured E coli

proteins were removed by centrifugation The enzyme was

further purified by column chromatography on a Sepharose

QFF column The protein was > 96% pure, as measured

by SDS⁄ PAGE

Crystallography

The protein was crystallized by the standing drop vapor

diffusion method Five microlitres of the enzyme, in 50 mm

Tris buffer, pH 7.5, was mixed with 5 lL of the

crystalliza-tion buffer containing 15% (w⁄ v) PEG 4000, 15% (v ⁄ v)

PEG 400, 0.2 m MgSO4, and 50 mm (NH4)2SO4, in 50 mm

cacodylate buffer, pH 8 The crystals appeared in 1 week

and had the morphology of chunky prisms with a lattice

organized by P21symmetry Mixing 5 lL of the enzyme in

50 mm Tris, pH 7.5, with 5 lL of the crystallization buffer

containing 15% (v⁄ v) PEG 400 0.2 m sodium tartrate, and

0.2 m (NH4)2SO4in 50 mm citrate, pH 5.6, resulted in

crys-tals with the morphology of thin plates characterized by the

P212121space group The data were collected to 2.2 A˚

reso-lution for the first crystal form, and to 2.4 A˚ for the second

form, on the RaxisIV++ area detector mounted on the Rigaku rotating anode at the X-ray facility at Rice Univer-sity (Houston, TX, USA) The structure was solved by molecular replacement (molrep), using the model construc-ted from the structures of several IMPases (human, MJ0109 and AF2372) as search probes The sequence of TM1415 shares the highest similarity to human IMPase ( 26% identity) and therefore this molecule was used as a scaffold However, there are three deletions (residues 70s, 160s and 210s), making it a bit shorter Those crucial dele-tions are shared with MJ0109 and AF2372 Therefore, we used those molecules to construct the fragments not corres-ponding well to the human structure The probe model was built from fragments of those proteins with the highest homology to TM1415 The full atom model was used for molecular replacement and later refined, using cns, to a standard R-factor of 0.209 and 0.178, as calculated on all reflections to 2.2 and 2.4 A˚ resolution, respectively, for forms 1 and 2 The data collection and refinement statistics can be found in Table 1

Sequence versus structure analysis

The iterated BLAST search was used to establish the mem-bers of the multifunctional IMPase family The groupings followed the CDD classification of the NCBI (http:// www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd) The seq-uence to 3D structure fit was estimated by the program psqs, developed at the Burnham Institute by A Godzik Predictions of the disorder were performed at the web ser-ver of the disprot (Dunker) [21]

We also carried out a clustering experiment in which we investigated the entire IMPase⁄ FBPase family The PFAM clan ‘inositol polyphosphate 1 phosphatase like superfamily’ includes three PFAM domain families (a) Inositol_P(PF00459), (b) FBPase(PF00316) and (c) FBPase_glpX(PF03320) The Inositol_P family has 65 sequences in its seed alignment, representing 586 proteins; and FBPase and FBPase_glpX each has 14 and 6 seed sequences, representing 233 and 101 proteins

Fig 5 Multisequence alignment of the loop fragments of all the family representatives, including T maritima and Homo sapiens Amino acids implicated in the catalytic mechanism are on a blue background The green and the light blue background mark conserved residues The secondary structure, as calculated by DSSP [26] is marked under the sequences, with red for the a-helix and orange for the b-sheet The figure was prepared using the program, VISSA [27].

Trang 8

All these 85 seed sequences were clustered into

sub-families at 25% sequence similarity and one representative

sequence was selected for each subfamily Within each

clus-ter, all the sequences were similar to the representative at

25% similarity or more, but similarities between all the

rep-resentatives of different clusters were below 25% The

clus-tering was performed with program cd-hit [24]

These 85 sequences were clustered into 13 subfamilies

Three families represented singletons, and another 10

sub-families contained 2–22 members Five subsub-families

con-tained proteins with 3D structures deposited in PDB The

average identity within each cluster was 35% Figure 4

shows the alignment of TM1415 (which belongs to the

IMPA1_HUMAN cluster) with representative proteins

from each cluster The initial alignment was made using

clustalw [25] and was edited according to the structural

alignment of five present in the PDB proteins

Acknowledgements

We would like to thank Dr Andrey Bobkov for help

in protein production and gel filtration experiments

This work was supported by the NIH grant

1R01 G64481 (to BS), National Science Foundation

grant MCB-9978250 (to MFR), and Department of

Energy Biosciences DE-FG02–91ER20025 (to MFR)

References

1 Zhang Y, Liang JY & Lipscomb WN (1993) Structural

similarities between fructose-1,6-bisphosphatase and

ino-sitol monophosphatase Biochem Biophys Res Commun

190, 1080–1083

2 York JD, Ponder JW & Majerus PW (1995) Definition

of a metal-dependent⁄ Li(+)-inhibited

phosphomono-esterase protein family based upon a conserved

three-dimensional core structure Proc Natl Acad Sci USA 92,

5149–5153

3 Chen L & Roberts MF (2000) Overexpression,

purifica-tion and analysis of complementapurifica-tion behavior of E

coliSuhB protein: Comparison with bacterial and

archaeal inositol monophosphatases Biochemistry 39,

4145–4153

4 Nimmo HG & Tipton KF (1975) The allosteric

proper-ties of beef-liver fructose bisphosphatase Eur J Biochem

58, 575–585

5 Villeret V, Huang S, Zhang Y, Xue Y & Lipscomb WN

(1995) Crystal structure of spinach chloroplast

fructose-1,6-bisphosphatase at 2.8 A˚ resolution Biochemistry 34,

4299–4306

6 Chen L & Roberts MF (1999) Characterization of a

tetrameric inositol monophosphatase from the

hyperthermophilic bacterium Thermotoga maritima

Appl Environ Microbiol 65, 4559–4567

7 Stec B, Yang H, Johnson KA, Chen L & Roberts MF (2000) MJ0109 is an enzyme that is both an inositol monophosphatase and the ‘missing’ archaeal fructose-1, 6-bisphosphatase Nat Struct Biol 7, 1046–1050

8 Johnson KA, Chen L, Yang H, Roberts MF & Stec B (2001) Crystal structure and catalytic mechanism of the MJ0109 gene product: a bifunctional enzyme with inosi-tol monophosphatase and fructose 1,6-bisphosphatase activities Biochemistry 40, 618–630

9 Stieglitz KA, Johnson KA, Yang H, Roberts MF, Seaton BA, Head JF & Stec B (2002) Crystal structure

of a dual activity IMPase⁄ FBPase (AF2372) from Archaeoglobus fulgidus The story of a mobile loop

J Biol Chem 277, 22863–22874

10 Choe JY, Fromm HJ & Honzatko RB (2000) Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes Biochemistry 39, 8565–8574

11 Hallcher LM & Sherman WR (1980) The effects of lithium ion and other agents on the activity of myo-ino-sitol-1-phosphatase from bovine brain J Biol Chem 255, 10896–10901

12 Bone R, Springer JP & Atack JR (1992) Structure of inositol monophosphatase, the putative target of lithium therapy Proc Natl Acad Sci USA 89, 10031–10035

13 Patel S, Yenush L, Rodriguez PL, Serrano R & Blundell

TL (2002) Crystal structure of an enzyme displaying both inositol-polyphosphate-1-phosphatase and 3¢-phos-phoadenosine-5¢-phosphate phosphatase activities: a novel target of lithium therapy J Mol Biol 315, 677– 685

14 Fieve RR (1999) Lithium therapy at the millennium: a revolutionary drug used for 50 years faces competing options and possible demise Bipolar Disord 1, 67–70

15 Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM & Obradovic Z (2002) Intrinsic disordered and protein function Biochemistry 41, 6573–6582

16 Dyson HJ & Wright PE (2005) Intrinsically unstruc-tured proteins and their functions Nat Rev Mol Cell Biol 6, 197–208

17 Vagin A & Teplyakov A (1997) MOLREP: an auto-mated program for molecular replacement J Appl Cryst

30, 1022–1025

18 Brunger AT, Adams PD, Clore GM, DeLano WL, Gros

P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges

M, Pannu NS et al (1998) Crystallography & NMR system: a new software suite for macromolecular struc-ture determination Acta Crystallogr D 54, 905–921

19 Laskowski RA, MacArthur MW, Moss DS & Thornton

JM (1993) PROCHECK: a program to check the stereo-chemical quality of protein structures J Appl Cryst 26, 283–291

20 Lu G, Stec B, Giroux EL & Kantrowitz ER (1996) Evidence for an active T-state pig kidney fructose

Trang 9

1,6-bisphosphatase: interface residue Lys-42 is important

for allosteric inhibition and AMP cooperativity Protein

Sci 5, 2333–2342

21 Zhang Y, Liang J-Y, Huang S & Lipscomb WN (1994)

Toward a mechanism for the allosteric transition of pig

kidney fructose-1,6-bisphosphatase J Mol Biol 244,

609–624

22 Dunker AK, Lawson JD, Brown CJ, Williams RM,

Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff

CM, Hipps KW et al (2001) Intrinsically disordered

protein J Mol Graph Model 19, 26–59

23 Siebert X & Amzel LM (2004) Loss of translational

entropy in molecular associations Proteins: Struct Funct

Genet 54, 104–115

24 Li W, Jaroszewski L & Godzik A (2001) Clustering of

highly homologous sequences to reduce the size of large

protein databases Bioinformatics 17, 282–283

25 Thompson JD, Higgins DG & Gibson TJ (1994)

clustal w: improving the sensitivity of progressive

multiple sequence alignment through sequence

weighting, position-specific gap penalties and weight

matrix choice Nucleic Acids Res 22, 4673–4680

26 Kabsch W & Sander C (1983) Dictionary of protein

sec-ondary structure: pattern recognition of

hydrogen-bonded and geometrical features Biopolymers 22,

2577–2637

27 Li W & Godzik A (2006) VISSA: a program to visualize

structural features from structure sequence alignment

Bioinformatics 22, 887–888

Supplementary material

The following supplementary material is available online:

Fig S1 Sigma-weighted 2Fo-Fc electron density, con-toured at the 1.1 r level covering the active site loop (residues 22-42), the active site residues (65-66, 79-84) and the ligands bound

Fig S2 Ribbon representation of a single monomer of the TM1415 (left) and the pig FBPase (right)

Fig S3 Temperature factor plots for both crystal forms

Fig S4 Diagram representing the disorder-score, as calculated by the program disprot (Dunker) [22] Fig S5 The chromatogram obtained from gel filtra-tion experiments carried out in citrate buffer (pH 5.6)

on a Superdex 200 column

This material is available as part of the online article from http://www.blackwell-synergy.com

Please note: Blackwell Publishing is not responsible for the content or functionality of any supplementary materials supplied by the authors Any queries (other than missing material) should be directed to the corres-ponding author for the article

Ngày đăng: 16/03/2014, 11:20

TỪ KHÓA LIÊN QUAN

TÀI LIỆU CÙNG NGƯỜI DÙNG

TÀI LIỆU LIÊN QUAN

🧩 Sản phẩm bạn có thể quan tâm