spacer
spacer

PDBsum entry 1o2d

Go to PDB code: 
protein ligands metals links
Oxidoreductase PDB id
1o2d
Jmol
Contents
Protein chains
359 a.a. *
Ligands
NAP ×2
TRS ×2
Metals
_FE ×2
Waters ×892
* Residue conservation analysis
PDB id:
1o2d
Name: Oxidoreductase
Title: Crystal structure of alcohol dehydrogenase, iron-containing (tm0920) from thermotoga maritima at 1.30 a resolution
Structure: Alcohol dehydrogenase, iron-containing. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm0920. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.30Å     R-factor:   0.139     R-free:   0.170
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
R.Schwarzenbacher et al. (2004). Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution. Proteins, 54, 174-177. PubMed id: 14705036 DOI: 10.1002/prot.10594
Date:
27-Feb-03     Release date:   10-Jun-03    
Supersedes: 1j5r
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X022  (Q9X022_THEMA) -  Alcohol dehydrogenase
Seq:
Struc:
359 a.a.
359 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1002/prot.10594 Proteins 54:174-177 (2004)
PubMed id: 14705036  
 
 
Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution.
R.Schwarzenbacher, F.von Delft, J.M.Canaves, L.S.Brinen, X.Dai, A.M.Deacon, M.A.Elsliger, S.Eshaghi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, C.Guda, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, D.McMullan, T.M.McPhillips, M.A.Miller, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, A.Robb, K.Rodrigues, T.L.Selby, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM0920. A: Ribbon diagram of Thermotoga maritima TM0920 1,3-propanediol dehydrogenase color coded from N-terminus (blue) to C-terminus (red) showing the domain organization and location of the active site (arrow). -helices (H1-H19) and -strands ( 1- 8) are indicated. The NADP^+ molecule is shown in ball and stick. The Fe^2+ ion is shown as a sphere in magenta. B: Diagram showing the secondary structure elements in TM0920 superimposed on its primary sequence. Residues located in the active site and interacting with Fe^2+ are indicated by blue dots and green triangles. Residues interacting with NADP^+ are indicated by red dots. The location of the -hairpin formed by -strands 6 and 7 is depicted in red.
Figure 2.
Figure 2. A: Schematic representation of the interactions between NADP^+ and its interacting residues. The NADP^+ molecule is depicted in purple and the protein residues are in orange. The atoms are indicated as follows: carbon (black), oxygen (red), nitrogen (blue), and phosphorus (purple). Hydrogen bonds are represented as dashed green lines. Residues implicated in hydrophobic interaction are represented as barbed circle sections. B: Close-up view of the active site showing residues coordinating the metal ion.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 174-177) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20924577 L.R.Jarboe (2011).
YqhD: a broad-substrate range aldehyde reductase with various applications in production of biorenewable fuels and chemicals.
  Appl Microbiol Biotechnol, 89, 249-257.  
19609521 S.Atsumi, T.Y.Wu, E.M.Eckl, S.D.Hawkins, T.Buelter, and J.C.Liao (2010).
Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes.
  Appl Microbiol Biotechnol, 85, 651-657.  
19011020 D.Marçal, A.T.Rêgo, M.A.Carrondo, and F.J.Enguita (2009).
1,3-Propanediol dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity.
  J Bacteriol, 191, 1143-1151.
PDB code: 3bfj
19383697 X.Liu, Y.Dong, J.Zhang, A.Zhang, L.Wang, and L.Feng (2009).
Two novel metal-independent long-chain alkyl alcohol dehydrogenases from Geobacillus thermodenitrificans NG80-2.
  Microbiology, 155, 2078-2085.  
19115036 X.Ying, A.M.Grunden, L.Nie, M.W.Adams, and K.Ma (2009).
Molecular characterization of the recombinant iron-containing alcohol dehydrogenase from the hyperthermophilic Archaeon, Thermococcus strain ES1.
  Extremophiles, 13, 299-311.  
17294170 X.Ying, Y.Wang, H.R.Badiei, V.Karanassios, and K.Ma (2007).
Purification and characterization of an iron-containing alcohol dehydrogenase in extremely thermophilic bacterium Thermotoga hypogea.
  Arch Microbiol, 187, 499-510.  
16917525 R.Sparling, R.Islam, N.Cicek, C.Carere, H.Chow, and D.B.Levin (2006).
Formate synthesis by Clostridium thermocellum during anaerobic fermentation.
  Can J Microbiol, 52, 681-688.  
15995211 C.Montella, L.Bellsolell, R.Pérez-Luque, J.Badía, L.Baldoma, M.Coll, and J.Aguilar (2005).
Crystal structure of an iron-dependent group III dehydrogenase that interconverts L-lactaldehyde and L-1,2-propanediol in Escherichia coli.
  J Bacteriol, 187, 4957-4966.
PDB codes: 2bi4 2bl4
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.  
15572776 P.H.Zwart, G.G.Langer, and V.S.Lamzin (2004).
Modelling bound ligands in protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 60, 2230-2239.  
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.