PDBsum entry 2b8n

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protein Protein-protein interface(s) links
Transferase PDB id
Protein chains
414 a.a. *
Waters ×97
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of glycerate kinase (ec (tm1585) thermotoga maritima at 2.70 a resolution
Structure: Glycerate kinase, putative. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1585. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.53Å     R-factor:   0.185     R-free:   0.246
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
R.Schwarzenbacher et al. (2006). Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold. Proteins, 65, 243-248. PubMed id: 16865707 DOI: 10.1002/prot.21058
07-Oct-05     Release date:   08-Nov-05    
Supersedes: 1o0u
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9X1S1  (Q9X1S1_THEMA) -  D-glycerate 2-kinase
417 a.a.
414 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glycerate 2-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + D-glycerate = ADP + 2-phospho-D-glycerate
+ D-glycerate
+ 2-phospho-D-glycerate
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1002/prot.21058 Proteins 65:243-248 (2006)
PubMed id: 16865707  
Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold.
R.Schwarzenbacher, D.McMullan, S.S.Krishna, Q.Xu, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.McPhillips, A.T.Morse, K.Quijano, G.Spraggon, R.C.Stevens, H.van den Bedem, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. A: Reaction catalyzed by glycerate-2-kinase (EC 2.7.1.-). B: Crystal structure of TM1585. Stereo ribbon diagram of TM1585 monomer color-coded from N-terminus (blue) to C-terminus (red). Helices (H1-H16) and -strands ( 1- 12) are labeled. N- and C-terminal domains are denoted by A and B, respectively. C: Diagram showing the secondary structural elements in TM1585 superimposed on its primary sequence. The -helices, 3[10]-helix, -strands, -bulges, and -turns are indicated. The -hairpin is depicted as a red loop. Highly conserved residues in the putative active site are marked with a green triangle. N- and C-terminal domain residues are shown in blue and red, respectively. -strands from N- and C-terminal domains are designated in -sheets A and B, respectively.
Figure 2.
Figure 2. A: The putative active site of TM1585 is located in the cleft between the N-terminal Rossmann-like and C-terminal domains. The highly conserved residues from the Rossmann-like domain (Lys47, Asp189, and the glycine-rich loop 122-SGGGS-126) and the C-terminal domain (Glu312, Arg325, Asn326, Asp351, and Asn407) are shown in ball-and-stick representation. Atoms are colored as follows: carbon (grey), oxygen (red), and nitrogen (blue). B: Stereo diagram of a structural alignment of the Rossmann fold domains of TM1585 (residues 23-249, blue) and glycerate kinase from Neisseria meningitidis (residues 1-55 and 261-368, grey). C: Stereo diagram of the TM1585 C-terminal domain (residues 4-22 and 250-417), which belongs to a new fold.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 243-248) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18156253 C.Yang, D.A.Rodionov, I.A.Rodionova, X.Li, and A.L.Osterman (2008).
Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways.
  J Bacteriol, 190, 1773-1782.  
17563835 B.Liu, Y.Hong, L.Wu, Z.Li, J.Ni, D.Sheng, and Y.Shen (2007).
A unique highly thermostable 2-phosphoglycerate forming glycerate kinase from the hyperthermophilic archaeon Pyrococcus horikoshii: gene cloning, expression and characterization.
  Extremophiles, 11, 733-739.  
17764545 D.Kehrer, H.Ahmed, H.Brinkmann, and B.Siebers (2007).
Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes.
  BMC Genomics, 8, 301.  
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