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PDBsum entry 1feh
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Oxidoreductase
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PDB id
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1feh
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* Residue conservation analysis
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Enzyme class:
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E.C.1.12.7.2
- ferredoxin hydrogenase.
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Reaction:
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H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 reduced [2Fe-2S]-[ferredoxin] + 2 H+
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Cofactor:
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Iron-sulfur; Ni(2+)
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Iron-sulfur
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Ni(2+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Science
282:1853-1858
(1998)
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PubMed id:
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X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.
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J.W.Peters,
W.N.Lanzilotta,
B.J.Lemon,
L.C.Seefeldt.
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ABSTRACT
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A three-dimensional structure for the monomeric iron-containing hydrogenase
(CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by
x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing.
CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield
dihydrogen, was found to contain 20 gram atoms of iron per mole of protein,
clusters. The probable active-site cluster,
previously termed the H-cluster, was found to be an unexpected arrangement of
cubane subcluster covalently bridged by a
subcluster
both exist with an octahedral coordination geometry and are bridged to each
other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl
or cyanide molecule. This structure provides insights into the mechanism of
cluster
structure and function in biological systems.
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Selected figure(s)
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Figure 3.
Fig. 3. (A) Topology diagram of the [2Fe-2S]-containing FS2
domain in a side-by-side comparison with the [2Fe-2S] ferredoxin
from Chorella fusca. The proteins are shown from the same
relative perspective, with the FS2 domain shown in purple and
the C. fusca ferredoxin shown in orange. The [2Fe-2S] cluster is
shown as a space-filling model (colors as in Fig. 1A). (B)
Topology diagram of the 2-[4Fe-4S]-containing FS4A-FS4B domain
in a side-by-side comparison with the 2-[4Fe-4S] ferredoxin from
Chromatium vinosum. The proteins are shown from the same
relative perspective, with the FS4A-FS4B domain shown in green
and the C. vinosum ferredoxin shown in orange. The [4Fe-4S]
clusters are shown as space-filling models. (C) Topology diagram
of the [4Fe-4S]-containing FS4C domain, showing the location and
composition of the four coordinating ligands His94, Cys98,
Cys101, and Cys107.
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Figure 5.
Fig. 5. Stereo view of selected amino acid residues in the
polypeptide environment of the [2Fe] subcluster of HC (colors as
in Fig. 2). The [4Fe-4S] subcluster and associated ligand are
included to provide the proper perspective and are indicated in
light gray. C, Cys; F, Phe; K, Lys; S, Ser; M, Met.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1998,
282,
1853-1858)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Gao,
D.Y.Jiang,
Q.C.Liang,
and
Q.Duan
(2012).
Bis{μ-[4-(1,3-benzothia-zol-2-yl)phen-yl]methane-thiol-ato-κS,S':S,S'}bis-[tricarbonyl-iron(I)](Fe-Fe).
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Acta Crystallogr Sect E Struct Rep Online,
68,
m330.
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S.Gao,
Q.Duan,
and
D.Y.Jiang
(2012).
{μ-2-[4-(1,3-Benzothia-zol-2-yl)phen-yl]-2-aza-propane-1,3-dithiol-ato-κS,S':S,S'}bis-[tricarbonyl-iron(I)].
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Acta Crystallogr Sect E Struct Rep Online,
68,
m248.
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S.Gao,
Q.Duan,
and
D.Y.Jiang
(2012).
{μ-2-[4-(Benzothia-zol-2-yl)benz-yl]-2-aza-propane-1,3-dithiol-ato-1:2κS,S':S,S'}bis-[tricarbonyl-iron(I)].
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Acta Crystallogr Sect E Struct Rep Online,
68,
m315.
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A.R.Grossman,
C.Catalanotti,
W.Yang,
A.Dubini,
L.Magneschi,
V.Subramanian,
M.C.Posewitz,
and
M.Seibert
(2011).
Multiple facets of anoxic metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii.
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New Phytol,
190,
279-288.
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B.Friedrich,
J.Fritsch,
and
O.Lenz
(2011).
Oxygen-tolerant hydrogenases in hydrogen-based technologies.
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Curr Opin Biotechnol,
22,
358-364.
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C.Greco,
M.Bruschi,
P.Fantucci,
U.Ryde,
and
L.De Gioia
(2011).
Isocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]-Hydrogenases.
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Chemistry,
17,
1954-1965.
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D.Benito-Garagorri,
I.Lagoja,
L.F.Veiros,
and
K.A.Kirchner
(2011).
Reactivity of coordinatively unsaturated iron complexes towards carbon monoxide: to bind or not to bind?
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Dalton Trans,
40,
4778-4792.
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G.Hong,
A.J.Cornish,
E.L.Hegg,
and
R.Pachter
(2011).
On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations.
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Biochim Biophys Acta,
1807,
510-517.
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J.Saxena,
and
R.S.Tanner
(2011).
Effect of trace metals on ethanol production from synthesis gas by the ethanologenic acetogen, Clostridium ragsdalei.
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J Ind Microbiol Biotechnol,
38,
513-521.
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J.Zhu,
Y.Tang,
G.M.Jiang,
M.Wang,
and
P.Hua
(2011).
Penta-carbonyl-1κC,2κC-(4-iodo-phenyl isocyanide-1κC)(μ-propane-1,3-dithiol-ato-1:2κS,S':S,S')iron(I)(Fe-Fe).
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Acta Crystallogr Sect E Struct Rep Online,
67,
m1753-m1754.
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L.C.Song,
Z.J.Xie,
X.F.Liu,
J.B.Ming,
J.H.Ge,
X.G.Zhang,
T.Y.Yan,
and
P.Gao
(2011).
Synthetic and structural studies on new diiron azadithiolate (ADT)-type model compounds for active site of [FeFe]hydrogenases.
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Dalton Trans,
40,
837-846.
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P.L.Roach
(2011).
Radicals from S-adenosylmethionine and their application to biosynthesis.
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Curr Opin Chem Biol,
15,
267-275.
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S.Lounissi,
J.F.Capon,
F.Gloaguen,
F.Matoussi,
F.Y.Pétillon,
P.Schollhammer,
and
J.Talarmin
(2011).
Diiron species containing a cyclic P(Ph)2N(Ph)2 diphosphine related to the [FeFe]H2ases active site.
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Chem Commun (Camb),
47,
878-880.
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Y.C.Liu,
L.K.Tu,
T.H.Yen,
G.H.Lee,
and
M.H.Chiang
(2011).
Influences on the rotated structure of diiron dithiolate complexes: electronic asymmetry vs. secondary coordination sphere interaction.
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Dalton Trans,
40,
2528-2541.
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Z.Xiao,
Z.Wei,
L.Long,
Y.Wang,
D.J.Evans,
and
X.Liu
(2011).
Diiron carbonyl complexes possessing a {Fe(II)Fe(II)} core: synthesis, characterisation, and electrochemical investigation.
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Dalton Trans,
40,
4291-4299.
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A.Begum,
G.Moula,
and
S.Sarkar
(2010).
A nickel(II)-sulfur-based radical-ligand complex as a functional model of hydrogenase.
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Chemistry,
16,
12324-12327.
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A.Grigoropoulos,
and
R.K.Szilagyi
(2010).
Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster.
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J Biol Inorg Chem,
15,
1177-1182.
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A.Jablonskyte,
J.A.Wright,
and
C.J.Pickett
(2010).
Mechanistic aspects of the protonation of [FeFe]-hydrogenase subsite analogues.
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Dalton Trans,
39,
3026-3034.
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C.M.Agapakis,
D.C.Ducat,
P.M.Boyle,
E.H.Wintermute,
J.C.Way,
and
P.A.Silver
(2010).
Insulation of a synthetic hydrogen metabolism circuit in bacteria.
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J Biol Eng,
4,
3.
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C.Zhan,
X.Wang,
Z.Wei,
D.J.Evans,
X.Ru,
X.Zeng,
and
X.Liu
(2010).
Synthesis and characterisation of polymeric materials consisting of {Fe2(CO)5}-unit and their relevance to the diiron sub-unit of [FeFe]-hydrogenase.
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Dalton Trans,
39,
11255-11262.
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C.Zheng,
K.Kim,
T.Matsumoto,
and
S.Ogo
(2010).
The useful properties of H2O as a ligand of a hydrogenase mimic.
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Dalton Trans,
39,
2218-2225.
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D.W.Mulder,
E.S.Boyd,
R.Sarma,
R.K.Lange,
J.A.Endrizzi,
J.B.Broderick,
and
J.W.Peters
(2010).
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG).
|
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Nature,
465,
248-251.
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PDB code:
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E.M.Shepard,
S.E.McGlynn,
A.L.Bueling,
C.S.Grady-Smith,
S.J.George,
M.A.Winslow,
S.P.Cramer,
J.W.Peters,
and
J.B.Broderick
(2010).
Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold.
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Proc Natl Acad Sci U S A,
107,
10448-10453.
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H.Zhang,
D.Chen,
Y.Zhang,
G.Zhang,
and
J.Liu
(2010).
On the mechanism of carbonyl hydrogenation catalyzed by iron catalyst.
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Dalton Trans,
39,
1972-1978.
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J.A.Stapleton,
and
J.R.Swartz
(2010).
A cell-free microtiter plate screen for improved [FeFe] hydrogenases.
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PLoS One,
5,
e10554.
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J.A.Stapleton,
and
J.R.Swartz
(2010).
Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases.
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PLoS One,
5,
e15275.
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J.M.Kuchenreuther,
C.S.Grady-Smith,
A.S.Bingham,
S.J.George,
S.P.Cramer,
and
J.R.Swartz
(2010).
High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli.
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PLoS One,
5,
e15491.
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J.P.Bigi,
T.E.Hanna,
W.H.Harman,
A.Chang,
and
C.J.Chang
(2010).
Electrocatalytic reduction of protons to hydrogen by a water-compatible cobalt polypyridyl platform.
|
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Chem Commun (Camb),
46,
958-960.
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M.Calusinska,
T.Happe,
B.Joris,
and
A.Wilmotte
(2010).
The surprising diversity of clostridial hydrogenases: a comparative genomic perspective.
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Microbiology,
156,
1575-1588.
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M.G.Galinato,
C.M.Whaley,
and
N.Lehnert
(2010).
Vibrational analysis of the model complex (mu-edt)[Fe(CO)(3)](2) and comparison to iron-only hydrogenase: the activation scale of hydrogenase model systems.
|
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Inorg Chem,
49,
3201-3215.
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M.Q.Hu,
H.M.Wen,
C.B.Ma,
N.Li,
Q.Y.Yan,
H.Chen,
and
C.N.Chen
(2010).
Synthesis, structures and electrochemistry studies of 2Fe2S-Fe(ii)(S-2N)(2) models for H-cluster of [FeFe]-hydrogenase.
|
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Dalton Trans,
39,
9484-9486.
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M.Saggu,
C.Teutloff,
M.Ludwig,
M.Brecht,
M.E.Pandelia,
O.Lenz,
B.Friedrich,
W.Lubitz,
P.Hildebrandt,
F.Lendzian,
and
R.Bittl
(2010).
Comparison of the membrane-bound [NiFe] hydrogenases from R. eutropha H16 and D. vulgaris Miyazaki F in the oxidized ready state by pulsed EPR.
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Phys Chem Chem Phys,
12,
2139-2148.
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M.Saggu,
M.Ludwig,
B.Friedrich,
P.Hildebrandt,
R.Bittl,
F.Lendzian,
O.Lenz,
and
I.Zebger
(2010).
Impact of amino acid substitutions near the catalytic site on the spectral properties of an O2-tolerant membrane-bound [NiFe] hydrogenase.
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Chemphyschem,
11,
1215-1224.
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P.Surawatanawong,
J.W.Tye,
M.Y.Darensbourg,
and
M.B.Hall
(2010).
Mechanism of electrocatalytic hydrogen production by a di-iron model of iron-iron hydrogenase: a density functional theory study of proton dissociation constants and electrode reduction potentials.
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Dalton Trans,
39,
3093-3104.
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R.K.Thauer,
A.K.Kaster,
M.Goenrich,
M.Schick,
T.Hiromoto,
and
S.Shima
(2010).
Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage.
|
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Annu Rev Biochem,
79,
507-536.
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S.E.McGlynn,
E.S.Boyd,
E.M.Shepard,
R.K.Lange,
R.Gerlach,
J.B.Broderick,
and
J.W.Peters
(2010).
Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor.
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J Bacteriol,
192,
595-598.
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S.Ezzaher,
A.Gogoll,
C.Bruhn,
and
S.Ott
(2010).
Directing protonation in [FeFe] hydrogenase active site models by modifications in their second coordination sphere.
|
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Chem Commun (Camb),
46,
5775-5777.
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T.Kanazuru,
E.F.Sato,
K.Nagata,
H.Matsui,
K.Watanabe,
E.Kasahara,
M.Jikumaru,
J.Inoue,
and
M.Inoue
(2010).
Role of hydrogen generation by Klebsiella pneumoniae in the oral cavity.
|
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J Microbiol,
48,
778-783.
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U.P.Apfel,
M.Rudolph,
C.Apfel,
C.Robl,
D.Langenegger,
D.Hoyer,
B.Jaun,
M.O.Ebert,
T.Alpermann,
D.Seebach,
and
W.Weigand
(2010).
Reaction of Fe3(CO)12 with octreotide--chemical, electrochemical and biological investigations.
|
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Dalton Trans,
39,
3065-3071.
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W.G.Wang,
F.Wang,
H.Y.Wang,
G.Si,
C.H.Tung,
and
L.Z.Wu
(2010).
Photocatalytic hydrogen evolution by [FeFe] hydrogenase mimics in homogeneous solution.
|
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Chem Asian J,
5,
1796-1803.
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W.Gao,
J.Sun,
T.Akermark,
M.Li,
L.Eriksson,
L.Sun,
and
B.Akermark
(2010).
Attachment of a hydrogen-bonding carboxylate side chain to an [FeFe]-hydrogenase model complex: influence on the catalytic mechanism.
|
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Chemistry,
16,
2537-2546.
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A.J.Shaw,
D.A.Hogsett,
and
L.R.Lynd
(2009).
Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout.
|
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J Bacteriol,
191,
6457-6464.
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A.Le Goff,
V.Artero,
B.Jousselme,
P.D.Tran,
N.Guillet,
R.Métayé,
A.Fihri,
S.Palacin,
and
M.Fontecave
(2009).
From hydrogenases to noble metal-free catalytic nanomaterials for h2 production and uptake.
|
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Science,
326,
1384-1387.
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A.M.Kluwer,
R.Kapre,
F.Hartl,
M.Lutz,
A.L.Spek,
A.M.Brouwer,
P.W.van Leeuwen,
and
J.N.Reek
(2009).
Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.
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Proc Natl Acad Sci U S A,
106,
10460-10465.
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A.Silakov,
B.Wenk,
E.Reijerse,
S.P.Albracht,
and
W.Lubitz
(2009).
Spin distribution of the H-cluster in the H(ox)-CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of (14)N and (13)C nuclear interactions.
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J Biol Inorg Chem,
14,
301-313.
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A.Silakov,
B.Wenk,
E.Reijerse,
and
W.Lubitz
(2009).
(14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge.
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Phys Chem Chem Phys,
11,
6592-6599.
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D.Dogaru,
S.Motiu,
and
V.Gogonea
(2009).
Inactivation of [Fe-Fe]-Hydrogenase by O(2). Thermodynamics and Frontier Molecular Orbitals Analyses.
|
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Int J Quantum Chem,
109,
876-889.
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D.Dogaru,
S.Motiu,
and
V.Gogonea
(2009).
Residue Mutations in [Fe-Fe]-hydrogenase Impedes O(2) Binding: A QM/MM Investigation.
|
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Int J Quantum Chem,
110,
1784-1792.
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E.S.Boyd,
J.R.Spear,
and
J.W.Peters
(2009).
[FeFe] hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community.
|
| |
Appl Environ Microbiol,
75,
4620-4623.
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J.M.Kuchenreuther,
J.A.Stapleton,
and
J.R.Swartz
(2009).
Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation.
|
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PLoS One,
4,
e7565.
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M.L.Ghirardi,
A.Dubini,
J.Yu,
and
P.C.Maness
(2009).
Photobiological hydrogen-producing systems.
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(1999).
Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase.
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Curr Opin Struct Biol,
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The hydA gene encoding the H(2)-evolving hydrogenase of Clostridium perfringens: molecular characterization and expression of the gene.
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FEMS Microbiol Lett,
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M.P.Golinelli,
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Site-directed mutagenesis of the cysteine ligands to the [4Fe-4S] cluster of Escherichia coli MutY.
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| |
Biochemistry,
38,
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R.Morales,
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Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes.
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| |
Biochemistry,
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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.
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');
}
}
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