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PDBsum entry 1s20

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1s20
Jmol
Contents
Protein chains
(+ 2 more) 334 a.a. *
Ligands
TLA ×6
NAD ×6
Waters ×1401
* Residue conservation analysis
PDB id:
1s20
Name: Oxidoreductase
Title: A novel NAD binding protein revealed by the crystal structure of e. Coli 2,3-diketogulonate reductase (yiak) northeast structural genomics consortium target er82
Structure: Hypothetical oxidoreductase yiak. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: yiak, b3575. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.191     R-free:   0.250
Authors: F.Forouhar,I.Lee,J.Benach,K.Kulkarni,R.Xiao,T.B.Acton, G.T.Montelione,L.Tong,Northeast Structural Genomics Consortium (Nesg)
Key ref:
F.Forouhar et al. (2004). A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK). J Biol Chem, 279, 13148-13155. PubMed id: 14718529 DOI: 10.1074/jbc.M313580200
Date:
07-Jan-04     Release date:   20-Jan-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37672  (DLGD_ECOLI) -  2,3-diketo-L-gulonate reductase
Seq:
Struc:
332 a.a.
334 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.130  - 3-dehydro-L-gulonate 2-dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 3-dehydro-L-gulonate + NAD(P)(+) = (4R,5S)-4,5,6-trihydroxy-2,3- dioxohexanoate + NAD(P)H
3-dehydro-L-gulonate
Bound ligand (Het Group name = TLA)
matches with 64.00% similarity
+
NAD(P)(+)
Bound ligand (Het Group name = NAD)
matches with 91.00% similarity
= (4R,5S)-4,5,6-trihydroxy-2,3- dioxohexanoate
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M313580200 J Biol Chem 279:13148-13155 (2004)
PubMed id: 14718529  
 
 
A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK).
F.Forouhar, I.Lee, J.Benach, K.Kulkarni, R.Xiao, T.B.Acton, G.T.Montelione, L.Tong.
 
  ABSTRACT  
 
Escherichia coli YiaK catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH. It belongs to a large family of oxidoreductases that is conserved in archaea, bacteria, and eukaryotes but shows no sequence homology to other proteins. We report here the crystal structures at up to 2.0-A resolution of YiaK alone and in complex with NAD-tartrate. YiaK has a new polypeptide backbone fold and a novel mode of recognizing the NAD cofactor. In addition, NAD is bound in an unusual conformation, at the interface of a dimer of the enzyme. The crystallographic analysis unexpectedly revealed the binding of tartrate in the active site. Enzyme kinetics studies confirm that tartrate and the related D-malate are inhibitors of YiaK. In contrast to most other enzymes where substrate binding produces a more closed conformation, the binding of NAD-tartrate to YiaK produces a more open active site. The free enzyme conformation is incompatible with NAD binding. His(44) is likely the catalytic residue of the enzyme.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. The binding mode of tartrate. A, final 2F[o] - F[c] electron density at a 2.2-Å resolution for the tartrate molecule bound to monomer A, contoured at 1 . B, molecular surface of the active-site region of YiaK. The tartrate molecule is shown as a stick model in green. C, stereographic drawing of the interactions between tartrate and YiaK. Hydrogen-bonding interactions are indicated by the dashed lines. A was created with SETOR (24), B was created with GRASP (22), and C was created with Molscript (25) and Raster3D (26).
Figure 5.
FIG. 5. Conformational change in YiaK upon NAD binding. A, structural overlay of the monomers of the free enzyme (magenta) and the NAD-tartrate complex (yellow) of YiaK. B, molecular surface of the active-site region of YiaK in the free enzyme structure. The NAD and tartrate molecules as observed in the complex structure are shown for reference. C, the active site of the free enzyme structure. The two sulfate ions (SO[4]) bound in the active site are shown. The NAD-tartrate molecules are shown for reference. TAR, tartrate; arrows, point to the sulfate ions. A and C were created with Molscript (25) and Raster3D (26), and B was created with GRASP (22).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 13148-13155) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17222174 C.L.Linster, and E.Van Schaftingen (2007).
Vitamin C. Biosynthesis, recycling and degradation in mammals.
  FEBS J, 274, 1.  
17588214 F.Forouhar, A.Kuzin, J.Seetharaman, I.Lee, W.Zhou, M.Abashidze, Y.Chen, W.Yong, H.Janjua, Y.Fang, D.Wang, K.Cunningham, R.Xiao, T.B.Acton, E.Pichersky, D.F.Klessig, C.W.Porter, G.T.Montelione, and L.Tong (2007).
Functional insights from structural genomics.
  J Struct Funct Genomics, 8, 37-44.
PDB codes: 1rty 1sqs 1tm0 1zbp 2hd3 2nv4 2oys
16233829 H.Muramatsu, H.Mihara, M.Goto, I.Miyahara, K.Hirotsu, T.Kurihara, and N.Esaki (2005).
A new family of NAD(P)H-dependent oxidoreductases distinct from conventional Rossmann-fold proteins.
  J Biosci Bioeng, 99, 541-547.  
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 codes are shown on the right.