spacer
spacer

PDBsum entry 1vj1

Go to PDB code: 
protein links
Unknown function PDB id
1vj1
Jmol
Contents
Protein chain
341 a.a. *
Waters ×153
* Residue conservation analysis
PDB id:
1vj1
Name: Unknown function
Title: Crystal structure of putative NADPH-dependent oxidoreductase musculus at 2.10 a resolution
Structure: Putative NADPH-dependent oxidoreductase. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: zadh1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.182     R-free:   0.216
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.Levin et al. (2004). Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution. Proteins, 56, 629-633. PubMed id: 15229897 DOI: 10.1002/prot.20163
Date:
03-Dec-03     Release date:   09-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8VDQ1  (PTGR2_MOUSE) -  Prostaglandin reductase 2
Seq:
Struc:
351 a.a.
341 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.48  - 15-oxoprostaglandin 13-oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 11-alpha-hydroxy-9,15-dioxoprost-5-enoate + NAD(P)(+) = (5Z)-(13E)-11- alpha-hydroxy-9,15-dioxoprosta-5,13-dienoate + NAD(P)H
11-alpha-hydroxy-9,15-dioxoprost-5-enoate
+ NAD(P)(+)
= (5Z)-(13E)-11- alpha-hydroxy-9,15-dioxoprosta-5,13-dienoate
+ 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   3 terms 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     13-prostaglandin reductase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.20163 Proteins 56:629-633 (2004)
PubMed id: 15229897  
 
 
Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution.
I.Levin, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, T.Biorac, J.Cambell, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of 18204011. A: Stereo ribbon diagram of mouse 18204011 color-coded from N-terminus (blue) to C-terminus (red) showing the domain organization and location of the putative active site (arrow). Helices H1-H17, and -strands ( 1- 15) as well as -sheets A, B, C and beginning (C253) and end (P266) of the disordered loop are indicated. B: Diagram showing the secondary structure elements in 18204011 superimposed on its primary sequence. The strands in each -sheet are indicated by a red A, B, and C. -hairpins are depicted as red loops. Disordered regions are depicted by a dashed line with the corresponding sequence in brackets. -bulges are marked by ; -turns are marked by .
Figure 2.
Figure 2. A: Ribbon diagram of a superposition of 18204011 (mouse) and quinone oxidoreductase from E. coli (PDB: 1qor) grey. The structures were superimposed on their nucleotide-binding domains. The NADPH molecule bound to quinone oxidoreductase is shown in cpk mode. B: Close up view of the active site. The NADPH molecule and the sulfate bound to the active site of quinone oxidoreductase are shown in ball and stick. The active site tyrosine (Y52) as observed in quinone oxidoreductase from E. coli and its potential counterpart (Y64) in 18204011 (the Y64 side-chain has been modeled here due to disorder in the crystal structure) are shown in ball and stick.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 629-633) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18940825 A.J.Bordner (2008).
Predicting small ligand binding sites in proteins using backbone structure.
  Bioinformatics, 24, 2865-2871.  
19000823 Y.H.Wu, T.P.Ko, R.T.Guo, S.M.Hu, L.M.Chuang, and A.H.Wang (2008).
Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2.
  Structure, 16, 1714-1723.
PDB codes: 2zb3 2zb4 2zb7 2zb8
16633561 B.Youn, R.Camacho, S.G.Moinuddin, C.Lee, L.B.Davin, N.G.Lewis, and C.Kang (2006).
Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4.
  Org Biomol Chem, 4, 1687-1697.
PDB codes: 2cf5 2cf6
17028190 B.Youn, S.J.Kim, S.G.Moinuddin, C.Lee, D.L.Bedgar, A.R.Harper, L.B.Davin, N.G.Lewis, and C.Kang (2006).
Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970.
  J Biol Chem, 281, 40076-40088.
PDB codes: 2j3h 2j3i 2j3j 2j3k
16211510 D.McMullan, J.M.Canaves, K.Quijano, P.Abdubek, E.Nigoghossian, J.Haugen, H.E.Klock, J.Vincent, J.Hale, J.Paulsen, and S.A.Lesley (2005).
High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions.
  J Struct Funct Genomics, 6, 135-141.  
16211521 R.Page, A.M.Deacon, S.A.Lesley, and R.C.Stevens (2005).
Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins.
  J Struct Funct Genomics, 6, 209-217.  
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.