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PDBsum entry 1b9b

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1b9b
Jmol
Contents
Protein chains
252 a.a. *
Ligands
SO4 ×2
Waters ×52
* Residue conservation analysis
PDB id:
1b9b
Name: Isomerase
Title: Triosephosphate isomerase of thermotoga maritima
Structure: Protein (triosephosphate isomerase). Chain: a, b. Synonym: tim. Engineered: yes. Other_details: a sulfate molecule is observed in the active both subunits
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.85Å     R-factor:   0.211     R-free:   0.249
Authors: D.Maes,R.K.Wierenga
Key ref:
D.Maes et al. (1999). The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures. Proteins, 37, 441-453. PubMed id: 10591103 DOI: 10.1002/(SICI)1097-0134(19991115)37:3<441::AID-PROT11>3.3.CO;2-Z
Date:
09-Feb-99     Release date:   01-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36204  (PGKT_THEMA) -  Bifunctional PGK/TIM
Seq:
Struc:
 
Seq:
Struc:
654 a.a.
252 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.7.2.3  - Phosphoglycerate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Calvin Cycle (carbon fixation stages)
      Reaction: ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
ATP
+ 3-phospho-D-glycerate
= ADP
+ 3-phospho-D-glyceroyl phosphate
   Enzyme class 3: E.C.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
= glycerone phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1002/(SICI)1097-0134(19991115)37:3<441::AID-PROT11>3.3.CO;2-Z Proteins 37:441-453 (1999)
PubMed id: 10591103  
 
 
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, R.K.Wierenga.
 
  ABSTRACT  
 
The molecular mechanisms that evolution has been employing to adapt to environmental temperatures are poorly understood. To gain some further insight into this subject we solved the crystal structure of triosephosphate isomerase (TIM) from the hyperthermophilic bacterium Thermotoga maritima (TmTIM). The enzyme is a tetramer, assembled as a dimer of dimers, suggesting that the tetrameric wild-type phosphoglycerate kinase PGK-TIM fusion protein consists of a core of two TIM dimers covalently linked to 4 PGK units. The crystal structure of TmTIM represents the most thermostable TIM presently known in its 3D-structure. It adds to a series of nine known TIM structures from a wide variety of organisms, spanning the range from psychrophiles to hyperthermophiles. Several properties believed to be involved in the adaptation to different temperatures were calculated and compared for all ten structures. No sequence preferences, correlated with thermal stability, were apparent from the amino acid composition or from the analysis of the loops and secondary structure elements of the ten TIMs. A common feature for both psychrophilic and T. maritima TIM is the large number of salt bridges compared with the number found in mesophilic TIMs. In the two thermophilic TIMs, the highest amount of accessible hydrophobic surface is buried during the folding and assembly process.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A: Stereo view of the C[ ]-trace of the TmTIM tetramer, composed of two canonical dimers (blue and green), related by a crystallographic twofold axis. The contacts between the two canonical dimers are between residues of loop 5 and helix 5. The N- and C-termini of each subunit are indicated with N1, C1, N2, C2, N3, C3, N4, and C4. The active sites are marked by yellow spheres. B: Stereo view of the interdimeric interface. The labeled residues are involved in interdimeric contacts. Each residue label has the same color as the corresponding subunit in Figure 1A.
Figure 4.
Figure 4. Graphs displaying various parameters for each of the ten TIM structures. The horizontal axis displays the ten TIMs with increasing thermal stability. A: Average charge within a sphere of 7 Å at the N-terminal ends ( ) and C-terminal ends ( ) of the framework helices. B: Hydrophobic ASA of the folded monomer buried on assembly (Å^2) (see also Table VII). C: Number of hydrogen bonds (:10) ( ), number of salt bridges ( ), number of residues in salt bridges ( ), and number of residues in salt bridge networks (x) (the numbers have been normalized per dimer).

Table VII. Volumes, Cavities, ASA, and Hydrophobicity
Vm Tb Lm Pf Hu Ch Ye Ec Bs Tm
Molecular volume of the oligomer (Å^3) 65473 66800 67378 70203 65805 65012 65723 65522 65346 141695 Total volume of cavities in the oligomer (Å^3) 374 773 589 535 616 656 544 409 453 1594 Total volume of the hydrophobic cavities in the oligomer (Å^3) 204 287 248 206 308 425 216 287 252 896 Total number of structured atoms in the oligomer 3733 3766 3812 3914 3736 3734 3766 3772 3765 7948 Compactness^a (Å^3) 17.44 17.53 17.52 17.80 17.45 17.24 17.31 17.26 17.24 17.63 Total ASA of the folded oligomer (Å^2) 18586 19198 19230 20378 18725 19623 19017 19510 17671 37073 Hydrophobic ASA of the folded oligomer (Å^2) 10693 11304 11573 10455 10873 11330 10787 11430 9993 21050 % Hydrophobicity^b 57.5 58.9 60.2 51.3 58.1 57.7 56.7 58.6 56.5 56.8 Total ASA buried on folding of the monomer (Å^2) 27060 27376 27683 27569 26844 26378 26960 27165 28006 29457 Hydrophobic ASA buried on folding of the monomer (Å^2) 16015 16148 16322 16258 15867 15650 16093 16043 16599 17378 % Hydrophobicity^c 59.2 59.0 59.0 59.0 59.1 59.3 59.7 59.1 59.3 59.0 Total ASA of the folded monomer buried on assembly (Å^2) 1663 1533 1477 1648 1686 1603 1622 1635 1752 2295^e Hydrophobic ASA of the folded monomer buried on assembly (Å^2) 1071 1003 989 1092 1058 1032 932 965 1188 1599^f % Hydrophobicity^d 64.4 65.5 66.9 66.2 62.8 64.4 57.4 59.0 67.8 69.7

^a Compactness = molecular volume (excluding the cavity volumes) of the oligomer/total number of structured atoms in the oligomer. ^b % Hydrophobicity = (hydrophobic ASA of the oligomer/total ASA of the oligomer) · 100%. ^c % Hydrophobicity = (hydrophobic ASA buried on folding of the monomer/total ASA buried on folding of the monomer) · 100%. ^d % Hydrophobicity = (hydrophobic ASA of the folded monomer buried on assembly/total ASA of the folded monomer buried on assembly) · 100%. ^e 1758 Å^2 at the canonical monomer-monomer interface, 537 Å^2 at the new dimer-dimer interface. ^f 1229 Å^2 at the canonical monomer-monomer interface, 370 Å^2 at the new dimer-dimer interface.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 37, 441-453) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18373848 M.J.Cuneo, Y.Tian, M.Allert, and H.W.Hellinga (2008).
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.
  BMC Struct Biol, 8, 20.
PDB code: 2ioy
18513746 N.P.King, T.M.Lee, M.R.Sawaya, D.Cascio, and T.O.Yeates (2008).
Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon.
  J Mol Biol, 380, 181-192.
PDB codes: 2rif 2rih
17242514 P.Gayathri, M.Banerjee, A.Vijayalakshmi, S.Azeez, H.Balaram, P.Balaram, and M.R.Murthy (2007).
Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 63, 206-220.
PDB code: 2h6r
16978361 D.Mathur, G.Malik, and L.C.Garg (2006).
Biochemical and functional characterization of triosephosphate isomerase from Mycobacterium tuberculosis H37Rv.
  FEMS Microbiol Lett, 263, 229-235.  
16741995 S.Donnini, G.Groenhof, R.K.Wierenga, and A.H.Juffer (2006).
The planar conformation of a strained proline ring: a QM/MM study.
  Proteins, 64, 700-710.  
16533850 S.Melchionna, R.Sinibaldi, and G.Briganti (2006).
Explanation of the stability of thermophilic proteins based on unique micromorphology.
  Biophys J, 90, 4204-4212.  
15146481 G.López-Velázquez, D.Molina-Ortiz, N.Cabrera, G.Hernández-Alcántara, J.Peon-Peralta, L.Yépez-Mulia, R.Pérez-Montfort, and H.Reyes-Vivas (2004).
An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia.
  Proteins, 55, 824-834.  
12643278 K.Ogasahara, M.Ishida, and K.Yutani (2003).
Stimulated interaction between and subunits of tryptophan synthase from hyperthermophile enhances its thermal stability.
  J Biol Chem, 278, 8922-8928.  
  12760631 L.Jiménez, D.A.Fernández-Velasco, K.Willms, and A.Landa (2003).
A comparative study of biochemical and immunological properties of triosephosphate isomerase from Taenia solium and Sus scrofa.
  J Parasitol, 89, 209-214.  
12949104 Y.Xu, G.Feller, C.Gerday, and N.Glansdorff (2003).
Moritella cold-active dihydrofolate reductase: are there natural limits to optimization of catalytic efficiency at low temperature?
  J Bacteriol, 185, 5519-5526.  
11933070 G.Gianese, F.Bossa, and S.Pascarella (2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
  Proteins, 47, 236-249.  
12473121 G.S.Bell, R.J.Russell, H.Connaris, D.W.Hough, M.J.Danson, and G.L.Taylor (2002).
Stepwise adaptations of citrate synthase to survival at life's extremes. From psychrophile to hyperthermophile.
  Eur J Biochem, 269, 6250-6260.
PDB code: 1o7x
12006590 K.Maithal, G.Ravindra, H.Balaram, and P.Balaram (2002).
Inhibition of plasmodium falciparum triose-phosphate isomerase by chemical modification of an interface cysteine. Electrospray ionization mass spectrometric analysis of differential cysteine reactivities.
  J Biol Chem, 277, 25106-25114.  
12487631 M.Dumontier, K.Michalickova, and C.W.Hogue (2002).
Species-specific protein sequence and fold optimizations.
  BMC Bioinformatics, 3, 39.  
12070156 N.Maeda, T.Kanai, H.Atomi, and T.Imanaka (2002).
The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability.
  J Biol Chem, 277, 31656-31662.  
12107280 P.Mallick, D.R.Boutz, D.Eisenberg, and T.O.Yeates (2002).
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.
  Proc Natl Acad Sci U S A, 99, 9679-9684.  
11453986 B.Clantin, C.Tricot, T.Lonhienne, V.Stalon, and V.Villeret (2001).
Probing the role of oligomerization in the high thermal stability of Pyrococcus furiosus ornithine carbamoyltransferase by site-specific mutants.
  Eur J Biochem, 268, 3937-3942.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
11258928 H.Reyes-Vivas, G.Hernández-Alcantara, G.López-Velazquez, N.Cabrera, R.Pérez-Montfort, M.T.de Gómez-Puyou, and A.Gómez-Puyou (2001).
Factors that control the reactivity of the interface cysteine of triosephosphate isomerase from Trypanosoma brucei and Trypanosoma cruzi.
  Biochemistry, 40, 3134-3140.  
11266604 S.A.Maves, and S.G.Sligar (2001).
Understanding thermostability in cytochrome P450 by combinatorial mutagenesis.
  Protein Sci, 10, 161-168.  
11489901 T.C.Appleby, I.I.Mathews, M.Porcelli, G.Cacciapuoti, and S.E.Ealick (2001).
Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
  J Biol Chem, 276, 39232-39242.
PDB codes: 1jds 1jdt 1jdu 1jdv 1jdz 1je0 1je1 1jp7 1jpv
10785370 A.M.Lambeir, J.Backmann, J.Ruiz-Sanz, V.Filimonov, J.E.Nielsen, I.Kursula, B.V.Norledge, and R.K.Wierenga (2000).
The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.
  Eur J Biochem, 267, 2516-2524.
PDB code: 1qds
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.