PDBsum entry 2afb

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protein metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
329 a.a. *
_CA ×4
_NI ×6
Waters ×394
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of 2-dehydro-3- deoxygluconokinase (ec 2.7 (tm0067) from thermotoga maritima at 2.05 a resolution
Structure: 2-keto-3-deoxygluconate kinase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm0067. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
2.05Å     R-factor:   0.177     R-free:   0.230
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.I.Mathews et al. (2008). Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution. Proteins, 70, 603-608. PubMed id: 18004772 DOI: 10.1002/prot.21842
25-Jul-05     Release date:   14-Feb-06    
Supersedes: 1j5v
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9WXS2  (Q9WXS2_THEMA) -  2-dehydro-3-deoxygluconate kinase
339 a.a.
329 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 2-dehydro-3-deoxygluconokinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho- D-gluconate
+ 2-dehydro-3-deoxy-D-gluconate
+ 2-dehydro-3-deoxy-6-phospho- D-gluconate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     transferase activity     4 terms  


DOI no: 10.1002/prot.21842 Proteins 70:603-608 (2008)
PubMed id: 18004772  
Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.
I.I.Mathews, D.McMullan, 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, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.van den Bedem, D.Weekes, 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. Crystal structure of TM0067. (A) Ribbon diagram of TM0067 color-coded according to domains I (light blue), II (orange), and III (green). Helices (H1-H14) and -strands ( 1- 14) are labeled. The arrow indicates the location of the putative active site by homology with T. thermophilus [see Fig. 2(A)]. The N- and C-termini are labeled, and -sheets A and B are labeled in red. (B) Diagram showing the secondary structural elements in TM0067 superimposed on its primary sequence. Helices are labeled H1-H14. The -hairpins are depicted as red loops, and the -turns and -turns are indicated. The -strands from -sheet A are labeled with a red A, while those from -sheet B are labeled with a red B. Disordered regions are represented by dashed lines.
Figure 2.
Figure 2. Structural analysis of 2-keto-3-deoxygluconate kinase. (A) Stereo diagram of a structural alignment of TM0067 (blue) and 2-keto-3-deoxygluconate kinase from T. thermophilus (PDB: 1v1a, grey), with bound ADP and 2-keto-3-deoxygluconate (KDG) shown as spheres. (B) Stereo view of the active site, with ADP, KDG, and the interacting residues shown in sticks. Carbon atoms are colored light blue (TM0067), grey (T. thermophilus enzyme), or yellow (ADP and KDG). Nitrogen, oxygen, and phosphorus atoms are colored blue, red, and orange, respectively. TM0067 residues are labeled; corresponding residues in T. thermophilus are in parentheses. (C) Ribbon diagram of the TM0067 hexamer. TM0067 forms a trimer of dimers, where the flap region is shared between the monomers of each dimer. In each dimer, one of the monomers is colored, while the other is in grey.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 603-608) copyright 2008.