PDBsum entry 1h0h

Electron transport

PDB id

1h0h

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Contents

			Protein chains

					977 a.a. *


					214 a.a. *

			Ligands

					2MD ×2


					MGD ×2


					UNX ×2


					SF4 ×8


					EPE ×2

			Metals

					__W ×2


					_CA ×2

			Waters ×1708

* Residue conservation analysis

PDB id:

1h0h

Links

Name:

Electron transport

Title:

Tungsten containing formate dehydrogenase from desulfovibrio gigas

Structure:

Formate dehydrogenase subunit alpha. Chain: a, k. Synonym: fdh subunit alpha, formate dehydrogenase large subunit. Formate dehydrogenase subunit beta. Chain: b, l. Synonym: fdh subunit beta, formate dehydrogenase small subunit

Source:

Desulfovibrio gigas. Organism_taxid: 879. Strain: ncib 9332. Other_details: native protein. Strain: ncib 9332

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å

R-factor:

0.169

R-free:

0.201

Authors:

H.C.A.Raaijmakers

Key ref:

H.Raaijmakers et al. (2002). Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas. Structure, 10, 1261-1272. PubMed id: 12220497 DOI: 10.1016/S0969-2126(02)00826-2

Date:

19-Jun-02

Release date:

20-Feb-03

PROCHECK

	Headers

	References

Protein chains

Q934F5 (FDHA_MEGGA) - Formate dehydrogenase subunit alpha from Megalodesulfovibrio gigas

Seq: Struc:

Seq: Struc:					1012 a.a. 977 a.a.*

Protein chains

Q8GC87 (FDHB_MEGG1) - Formate dehydrogenase subunit beta from Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)

Seq: Struc:					215 a.a. 214 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

Chains A, K: E.C.1.17.1.9 - formate dehydrogenase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

formate + NAD⁺ = CO2 + NADH

formate

NAD(+)
Bound ligand (Het Group name = 2MD)
matches with 75.00% similarity

CO2

NADH
Bound ligand (Het Group name = MGD)
matches with 75.00% similarity

Cofactor:

Flavin; Iron-sulfur; Mo cation

Flavin	Iron-sulfur	Mo cation

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

reference

DOI no: 10.1016/S0969-2126(02)00826-2	Structure 10:1261-1272 (2002)
PubMed id: 12220497

Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
H.Raaijmakers, S.Macieira, J.M.Dias, S.Teixeira, S.Bursakov, R.Huber, J.J.Moura, I.Moura, M.J.Romão.

ABSTRACT

Desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, center. No small subunit ortholog containing clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H(+) by buried waters and protonable amino acids and for CO(2) through a hydrophobic channel.

Selected figure(s)



	Figure 3. Figure 3. Stereo Representation of the Overall Structure of DgW-FDH from D. gigasThe small domain (214 amino acid residues) is represented in purple, and the large domain (977 amino acid residues) is colored after its domain classification. Domain I (red) corresponds to residues 9-68, 575-603, and 647-734; domain II (green) contains residues 69-157, 410-574, and 604-646; domain III (yellow) is defined by residues 157-409; domain IV (blue) is defined by residues 735-977. Domain IV can be divided into two subdomains, IVa (residues 735-795) and IVb (residues 796-977). The insertions (relative to the homologous NAP and FDH-H structures) present in several domains are shown in gray.(B) Representation of the four "exploded" domains of the large 977 aa subunit.(C) Comparison of the domain organization of DgW-FDH, D. desulfuricans NAP, and E. coli FDH-H. The insertions in DgW-FDH are depicted as dashed areas.(D) Stereo Ca trace numbered every 20 residues for domains II and III (top).(E) Stereo Ca trace numbered every 20 residues for domains I and IV and for the small subunit (below).

Figure was selected by the author.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20819103

X.Zhang, E.G.Matson, and J.R.Leadbetter (2011).
Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood-feeding termites and a wood-feeding roach.

Environ Microbiol, 13, 307-323.

20645325

E.Cremades, J.Echeverría, and S.Alvarez (2010).
The trigonal prism in coordination chemistry.

Chemistry, 16, 10380-10396.

19452052

M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.

Dalton Trans, (), 4053-4068.

19360810

N.M.Cerqueira, P.J.Gonzalez, C.D.Brondino, M.J.Romão, C.C.Romão, I.Moura, and J.J.Moura (2009).
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase.

J Comput Chem, 30, 2466-2484.

19206188

S.Groysman, and R.H.Holm (2009).
Biomimetic Chemistry of Iron, Nickel, Molybdenum, and Tungsten in Sulfur-Ligated Protein Sites (dagger).

Biochemistry, 48, 2310-2320.

19020675

H.Sugimoto, and H.Tsukube (2008).
Chemical analogues relevant to molybdenum and tungsten enzyme reaction centres toward structural dynamics and reaction diversity.

Chem Soc Rev, 37, 2609-2619.

18096847

J.R.Andreesen, and K.Makdessi (2008).
Tungsten, the surprisingly positively acting heavy metal element for prokaryotes.

Ann N Y Acad Sci, 1125, 215-229.

18327621

S.Najmudin, P.J.González, J.Trincão, C.Coelho, A.Mukhopadhyay, N.M.Cerqueira, C.C.Romão, I.Moura, J.J.Moura, C.D.Brondino, and M.J.Romão (2008).
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.

J Biol Inorg Chem, 13, 737-753.

PDB codes:

2jim 2jio 2jip 2jiq 2jir 2v3v 2v45

16962969

D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.

Structure, 14, 1377-1388.

PDB code:

2ivf

16830149

H.C.Raaijmakers, and M.J.Romão (2006).
Formate-reduced E. coli formate dehydrogenase H: The reinterpretation of the crystal structure suggests a new reaction mechanism.

J Biol Inorg Chem, 11, 849-854.

PDB code:

2iv2

16218872

M.Boll, B.Schink, A.Messerschmidt, and P.M.Kroneck (2005).
Novel bacterial molybdenum and tungsten enzymes: three-dimensional structure, spectroscopy, and reaction mechanism.

Biol Chem, 386, 999.

16511024

O.Einsle, H.Niessen, D.J.Abt, G.Seiffert, B.Schink, R.Huber, A.Messerschmidt, and P.M.Kroneck (2005).
Crystallization and preliminary X-ray analysis of the tungsten-dependent acetylene hydratase from Pelobacter acetylenicus.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 299-301.

15028701

F.Peters, M.Rother, and M.Boll (2004).
Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans.

J Bacteriol, 186, 2156-2163.

15311335

J.J.Moura, C.D.Brondino, J.Trincão, and M.J.Romão (2004).
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases.

J Biol Inorg Chem, 9, 791-799.

12948771

M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.

Curr Opin Struct Biol, 13, 418-423.

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.