PDBsum entry 2iv2

Oxidoreductase

PDB id

2iv2

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Contents

			Protein chain

					697 a.a. *

			Ligands

					SF4


					2MD


					MGD


					UNX

			Metals

					_MO

			Waters ×267

* Residue conservation analysis

PDB id:

2iv2

Links

Name:

Oxidoreductase

Title:

Reinterpretation of reduced form of formate dehydrogenase h from e. Coli

Structure:

Formate dehydrogenase h. Chain: x. Synonym: formate dehydrogenase-h subunit alpha,fdh-h,formate- hydrogen-lyase-linked,selenocysteine-containing polypeptide. Engineered: yes. Other_details: reduced form (mo(iv), fe4s4(red)) of fdh-h

Source:

Escherichia coli. Organism_taxid: 562. Gene: fdhf, b4079, jw4040. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: fdh-h was expressed anaerobically

Resolution:

2.27Å

R-factor:

0.178

R-free:

0.226

Authors:

H.C.A.Raaijmakers,M.J.Romao

Key ref:

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. PubMed id: 16830149

Date:

08-Jun-06

Release date:

12-Jun-06

PROCHECK

	Headers

	References

Protein chain

P07658 (FDHF_ECOLI) - Formate dehydrogenase H from Escherichia coli (strain K12)

Seq: Struc:

Seq: Struc:					715 a.a. 697 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.1.17.98.4 - formate dehydrogenase (acceptor).

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

Reaction:

formate + A + H⁺ = AH2 + CO2

formate	+		+	H(+)	=	AH2	+	CO2

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

Added reference

	J Biol Inorg Chem 11:849-854 (2006)
PubMed id: 16830149

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

ABSTRACT

Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.

Literature references that cite this PDB file's key reference

PubMed id

Reference

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.

19549881

N.Wagener, A.J.Pierik, A.Ibdah, R.Hille, and H.Dobbek (2009).
The Mo-Se active site of nicotinate dehydrogenase.

Proc Natl Acad Sci U S A, 106, 11055-11060.

PDB code:

3hrd

19206188

S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.

Biochemistry, 48, 2310-2320.

18716757

I.Lüke, G.Butland, K.Moore, G.Buchanan, V.Lyall, S.A.Fairhurst, J.F.Greenblatt, A.Emili, T.Palmer, and F.Sargent (2008).
Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein.

Arch Microbiol, 190, 685-696.

18536726

M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.

Nat Struct Mol Biol, 15, 730-737.

PDB codes:

2vpw 2vpx 2vpy 2vpz

18314977

R.Sarangi, S.I.Gorelsky, L.Basumallick, H.J.Hwang, R.C.Pratt, T.D.Stack, Y.Lu, K.O.Hodgson, B.Hedman, and E.I.Solomon (2008).
Spectroscopic and density functional theory studies of the blue-copper site in M121SeM and C112SeC azurin: Cu-Se versus Cu-S bonding.

J Am Chem Soc, 130, 3866-3877.

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

18801467

S.W.Ragsdale, and E.Pierce (2008).
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.

Biochim Biophys Acta, 1784, 1873-1898.

17277802

T.L.Hendrickson (2007).
Easing selenocysteine into proteins.

Nat Struct Mol Biol, 14, 100-101.

17471372

X.Ma, C.Schulzke, H.G.Schmidt, and M.Noltemeyer (2007).
Structural, electrochemical and oxygen atom transfer properties of a molybdenum selenoether complex [Mo2O4(OC3H6SeC3H6O)2] and its thioether analogue [Mo2O4(OC3H6SC3H6O)2].

Dalton Trans, (), 1773-1780.

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.