PDBsum entry 1o2d

Oxidoreductase

PDB id: 1o2d

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

Protein chains

Q9X022  (Q9X022_THEMA) -  Alcohol dehydrogenase, iron-containing from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 359 a.a.

Struc: 359 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.1 - alcohol dehydrogenase.
• Reaction:
  1. a primary alcohol + NAD⁺ = an aldehyde + NADH + H⁺
  2. a secondary alcohol + NAD⁺ = a ketone + NADH + H⁺

primary alcohol + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = aldehyde + NADH + H(+)

secondary alcohol + NAD(+) (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) = ketone + NADH + H(+)

• Cofactor: Zn(2+) or Fe cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.