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PDBsum entry 1cc1

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1cc1
Jmol
Contents
Protein chains
275 a.a. *
487 a.a. *
Ligands
SF4 ×3
FCO
H2S
Metals
_NI
FE2
Waters ×319
* Residue conservation analysis
PDB id:
1cc1
Name: Oxidoreductase
Title: Crystal structure of a reduced, active form of the ni-fe-se hydrogenase from desulfomicrobium baculatum
Structure: Hydrogenase (small subunit). Chain: s. Synonym: cytochrome c3 hydrogenase. Hydrogenase (large subunit). Chain: l. Synonym: cytochrome c3 hydrogenase. Other_details: complexed with iron/sulfur cluster, carbonmo (dicyano) iron, hydrosulfuric acid
Source: Desulfomicrobium baculatum. Organism_taxid: 899. Strain: wild type. Cellular_location: periplasm. Cellular_location: periplasm
Biol. unit: Dimer (from PQS)
Resolution:
2.15Å     R-factor:   0.194     R-free:   0.248
Authors: E.Garcin,X.Vernede,E.C.Hatchikian,A.Volbeda,M.Frey,J.C.Fonte Camps
Key ref:
E.Garcin et al. (1999). The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Structure Fold Des, 7, 557-566. PubMed id: 10378275 DOI: 10.1016/S0969-2126(99)80072-0
Date:
03-Mar-99     Release date:   01-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13063  (PHSS_DESBA) -  Periplasmic [NiFeSe] hydrogenase small subunit
Seq:
Struc:
315 a.a.
275 a.a.*
Protein chain
Pfam   ArchSchema ?
P13065  (PHSL_DESBA) -  Periplasmic [NiFeSe] hydrogenase large subunit
Seq:
Struc:
514 a.a.
487 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains S, L: E.C.1.12.99.6  - Hydrogenase (acceptor).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2 + A = AH2
      Cofactor: Iron-sulfur; Nickel
Iron-sulfur
Nickel
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0969-2126(99)80072-0 Structure Fold Des 7:557-566 (1999)
PubMed id: 10378275  
 
 
The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
E.Garcin, X.Vernede, E.C.Hatchikian, A.Volbeda, M.Frey, J.C.Fontecilla-Camps.
 
  ABSTRACT  
 
hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and the reduced D. baculatum hydrogenases shows that in the reduced enzyme the nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition, the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent from the D. baculatum hydrogenase. We also observe higher-than-average temperature factors for both the active site nickel-selenocysteine ligand and the neighboring Glu18 residue, suggesting that both these moieties are involved in proton transfer between the active site and the molecular surface. Other hydrogenases are the presence of a third cluster found in the D. gigas enzyme, and a putative iron center that substitutes the magnesium ion that has already been hydrogenases. CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of hydrogenases.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The environment of the putative hydrogen sulfide molecule. Stereoview of the active site and the hydrogen sulfide molecule. The distance between the iron of the active site and the assigned hydrogen sulfide molecule, represented by a dotted line, is 6.7 Å. The hydrogen sulfide molecule is coordinated by residues Thr70L, Ala71L and Asn103L. This figure was made using TURBO-FRODO [42].
 
  The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 557-566) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286651 E.E.Battin, M.T.Zimmerman, R.R.Ramoutar, C.E.Quarles, and J.L.Brumaghim (2011).
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Synthetic and structural studies on new diiron azadithiolate (ADT)-type model compounds for active site of [FeFe]hydrogenases.
  Dalton Trans, 40, 837-846.  
20669037 C.Gutiérrez-Sánchez, O.Rüdiger, V.M.Fernández, A.L.De Lacey, M.Marques, and I.A.Pereira (2010).
Interaction of the active site of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough with carbon monoxide and oxygen inhibitors.
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20107663 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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20221533 J.Y.Yang, R.M.Bullock, W.G.Dougherty, W.S.Kassel, B.Twamley, D.L.DuBois, and M.Rakowski DuBois (2010).
Reduction of oxygen catalyzed by nickel diphosphine complexes with positioned pendant amines.
  Dalton Trans, 39, 3001-3010.  
20301175 M.E.Pandelia, H.Ogata, and W.Lubitz (2010).
Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site.
  Chemphyschem, 11, 1127-1140.  
20147622 Y.Ohki, K.Yasumura, M.Ando, S.Shimokata, and K.Tatsumi (2010).
A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of CO3Fe(micro-StBu)3Ni{SC6H3-2,6-(mesityl)2} and reversible CO addition at the Ni site.
  Proc Natl Acad Sci U S A, 107, 3994-3997.  
19173074 A.Perra, Q.Wang, A.J.Blake, E.S.Davies, J.McMaster, C.Wilson, and M.Schröder (2009).
Unusual formation of a [NiSFe(2)(CO)(6)] cluster: a structural model for the inactive form of [NiFe] hydrogenase.
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19548119 E.E.Battin, and J.L.Brumaghim (2009).
Antioxidant activity of sulfur and selenium: a review of reactive oxygen species scavenging, glutathione peroxidase, and metal-binding antioxidant mechanisms.
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Overexpression, isolation, and spectroscopic characterization of the bidirectional [NiFe] hydrogenase from Synechocystis sp. PCC 6803.
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Structure-function relationships of anaerobic gas-processing metalloenzymes.
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The roles of the first and second coordination spheres in the design of molecular catalysts for H(2) production and oxidation.
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19304663 M.Saggu, I.Zebger, M.Ludwig, O.Lenz, B.Friedrich, P.Hildebrandt, and F.Lendzian (2009).
Spectroscopic Insights into the Oxygen-tolerant Membrane-associated [NiFe] Hydrogenase of Ralstonia eutropha H16.
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19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic Chemistry of Iron, Nickel, Molybdenum, and Tungsten in Sulfur-Ligated Protein Sites (dagger).
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19130447 S.Pal, Y.Ohki, T.Yoshikawa, K.Kuge, and K.Tatsumi (2009).
Dithiolate-bridged Fe-Ni-Fe trinuclear complexes consisting of Fe(CO)(3-n)(CN)(n) (n = 0, 1) components relevant to the active site of [NiFe] hydrogenase.
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19363030 S.W.Ragsdale (2009).
Nickel-based Enzyme Systems.
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18704522 A.L.De Lacey, C.Gutiérrez-Sánchez, V.M.Fernández, I.Pacheco, and I.A.Pereira (2008).
FTIR spectroelectrochemical characterization of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough.
  J Biol Inorg Chem, 13, 1315-1320.  
18647659 C.J.Chou, F.E.Jenney, M.W.Adams, and R.M.Kelly (2008).
Hydrogenesis in hyperthermophilic microorganisms: implications for biofuels.
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18378597 F.E.Jenney, and M.W.Adams (2008).
Hydrogenases of the model hyperthermophiles.
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18412257 I.Fdez Galván, A.Volbeda, J.C.Fontecilla-Camps, and M.J.Field (2008).
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase.
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18719950 I.Moura, S.R.Pauleta, and J.J.Moura (2008).
Enzymatic activity mastered by altering metal coordination spheres.
  J Biol Inorg Chem, 13, 1185-1195.  
18350177 P.Jayapal, D.Robinson, M.Sundararajan, I.H.Hillier, and J.J.McDouall (2008).
High level ab initio and DFT calculations of models of the catalytically active Ni-Fe hydrogenases.
  Phys Chem Chem Phys, 10, 1734-1738.  
18633545 P.Jayapal, M.Sundararajan, I.H.Hillier, and N.A.Burton (2008).
QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states.
  Phys Chem Chem Phys, 10, 4249-4257.  
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.
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18411840 S.Canaguier, V.Artero, and M.Fontecave (2008).
Modelling NiFe hydrogenases: nickel-based electrocatalysts for hydrogen production.
  Dalton Trans, (), 315-325.  
18653896 S.Shima, O.Pilak, S.Vogt, M.Schick, M.S.Stagni, W.Meyer-Klaucke, E.Warkentin, R.K.Thauer, and U.Ermler (2008).
The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.
  Science, 321, 572-575.
PDB codes: 3daf 3dag
18511566 Y.Ohki, K.Yasumura, K.Kuge, S.Tanino, M.Ando, Z.Li, and K.Tatsumi (2008).
Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase.
  Proc Natl Acad Sci U S A, 105, 7652-7657.  
17222178 A.Gebler, T.Burgdorf, A.L.De Lacey, O.Rüdiger, A.Martinez-Arias, O.Lenz, and B.Friedrich (2007).
Impact of alterations near the [NiFe] active site on the function of the H(2) sensor from Ralstonia eutropha.
  FEBS J, 274, 74-85.  
16969669 M.Long, J.Liu, Z.Chen, B.Bleijlevens, W.Roseboom, and S.P.Albracht (2007).
Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module.
  J Biol Inorg Chem, 12, 62-78.  
17082918 O.Schröder, B.Bleijlevens, T.E.de Jongh, Z.Chen, T.Li, J.Fischer, J.Förster, C.G.Friedrich, K.A.Bagley, S.P.Albracht, and W.Lubitz (2007).
Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans.
  J Biol Inorg Chem, 12, 212-233.  
16511689 A.Pardo, A.L.De Lacey, V.M.Fernández, H.J.Fan, Y.Fan, and M.B.Hall (2006).
Density functional study of the catalytic cycle of nickel-iron [NiFe] hydrogenases and the involvement of high-spin nickel(II).
  J Biol Inorg Chem, 11, 286-306.  
16514453 A.Perra, E.S.Davies, J.R.Hyde, Q.Wang, J.McMaster, and M.Schröder (2006).
Electrocatalytic production of hydrogen by a synthetic model of [NiFe] hydrogenases.
  Chem Commun (Camb), (), 1103-1105.  
16418856 E.van der Linden, T.Burgdorf, A.L.de Lacey, T.Buhrke, M.Scholte, V.M.Fernandez, B.Friedrich, and S.P.Albracht (2006).
An improved purification procedure for the soluble [NiFe]-hydrogenase of Ralstonia eutropha: new insights into its (in)stability and spectroscopic properties.
  J Biol Inorg Chem, 11, 247-260.  
16621815 F.M.Valente, C.C.Almeida, I.Pacheco, J.Carita, L.M.Saraiva, and I.A.Pereira (2006).
Selenium is involved in regulation of periplasmic hydrogenase gene expression in Desulfovibrio vulgaris Hildenborough.
  J Bacteriol, 188, 3228-3235.  
16704340 J.F.Stolz, P.Basu, J.M.Santini, and R.S.Oremland (2006).
Arsenic and selenium in microbial metabolism.
  Annu Rev Microbiol, 60, 107-130.  
16292669 M.van Gastel, M.Stein, M.Brecht, O.Schröder, F.Lendzian, R.Bittl, H.Ogata, Y.Higuchi, and W.Lubitz (2006).
A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
  J Biol Inorg Chem, 11, 41-51.  
16391746 P.A.Stenson, A.Marin-Becerra, C.Wilson, A.J.Blake, J.McMaster, and M.Schröder (2006).
Formation of [(L)Ni(mu2-S)x{Fe(CO)3}x] adducts (x = 1 or 2): analogues of the active site of [NiFe] hydrogenase.
  Chem Commun (Camb), (), 317-319.  
15803334 A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, and J.C.Fontecilla-Camps (2005).
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
  J Biol Inorg Chem, 10, 239-249.
PDB codes: 1yq9 1yqw 1yrq
16187073 F.M.Valente, A.S.Oliveira, N.Gnadt, I.Pacheco, A.V.Coelho, A.V.Xavier, M.Teixeira, C.M.Soares, and I.A.Pereira (2005).
Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase.
  J Biol Inorg Chem, 10, 667-682.  
16286638 J.W.Tye, M.B.Hall, and M.Y.Darensbourg (2005).
Better than platinum? Fuel cells energized by enzymes.
  Proc Natl Acad Sci U S A, 102, 16911-16912.  
16045760 O.Duché, S.Elsen, L.Cournac, and A.Colbeau (2005).
Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O2 sensitive without affecting its transductory activity.
  FEBS J, 272, 3899-3908.  
15976866 P.P.Phadnis, and G.Mugesh (2005).
Internally stabilized selenocysteine derivatives: syntheses, 77Se NMR and biomimetic studies.
  Org Biomol Chem, 3, 2476-2481.  
15611882 S.Foerster, M.van Gastel, M.Brecht, and W.Lubitz (2005).
An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase.
  J Biol Inorg Chem, 10, 51-62.  
15764814 T.Buhrke, S.Löscher, O.Lenz, E.Schlodder, I.Zebger, L.K.Andersen, P.Hildebrandt, W.Meyer-Klaucke, H.Dau, B.Friedrich, and M.Haumann (2005).
Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16.
  J Biol Chem, 280, 19488-19495.  
15342627 B.Bleijlevens, T.Buhrke, E.van der Linden, B.Friedrich, and S.P.Albracht (2004).
The auxiliary protein HypX provides oxygen tolerance to the soluble [NiFe]-hydrogenase of ralstonia eutropha H16 by way of a cyanide ligand to nickel.
  J Biol Chem, 279, 46686-46691.  
14764097 E.van der Linden, B.W.Faber, B.Bleijlevens, T.Burgdorf, M.Bernhard, B.Friedrich, and S.P.Albracht (2004).
Selective release and function of one of the two FMN groups in the cytoplasmic NAD+-reducing [NiFe]-hydrogenase from Ralstonia eutropha.
  Eur J Biochem, 271, 801-808.  
15365900 M.Bruschi, L.De Gioia, G.Zampella, M.Reiher, P.Fantucci, and M.Stein (2004).
A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site.
  J Biol Inorg Chem, 9, 873-884.  
15082711 M.C.Posewitz, P.W.King, S.L.Smolinski, L.Zhang, M.Seibert, and M.L.Ghirardi (2004).
Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase.
  J Biol Chem, 279, 25711-25720.  
14688251 S.Dementin, B.Burlat, A.L.De Lacey, A.Pardo, G.Adryanczyk-Perrier, B.Guigliarelli, V.M.Fernandez, and M.Rousset (2004).
A glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase.
  J Biol Chem, 279, 10508-10513.  
12642671 M.Y.Darensbourg, E.J.Lyon, X.Zhao, and I.P.Georgakaki (2003).
The organometallic active site of [Fe]hydrogenase: models and entatic states.
  Proc Natl Acad Sci U S A, 100, 3683-3688.  
12829270 S.B.Mulrooney, and R.P.Hausinger (2003).
Nickel uptake and utilization by microorganisms.
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12045096 D.C.Rees (2002).
Great metalloclusters in enzymology.
  Annu Rev Biochem, 71, 221-246.  
11857710 D.Sellmann, F.Geipel, and F.W.Heinemann (2002).
(NEt(4))(2)[Fe(CN)(2)(CO)('S(3)')]: an iron thiolate complex modeling the [Fe(CN)(2)(CO)(S-Cys)(2)] site of [NiFe] hydrogenase centers.
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12039011 M.Stein, and W.Lubitz (2002).
Quantum chemical calculations of [NiFe] hydrogenase.
  Curr Opin Chem Biol, 6, 243-249.  
12399498 T.Burgdorf, A.L.De Lacey, and B.Friedrich (2002).
Functional analysis by site-directed mutagenesis of the NAD(+)-reducing hydrogenase from Ralstonia eutropha.
  J Bacteriol, 184, 6280-6288.  
11524134 P.M.Vignais, B.Billoud, and J.Meyer (2001).
Classification and phylogeny of hydrogenases.
  FEMS Microbiol Rev, 25, 455-501.  
11509713 R.K.Thauer (2001).
Enzymology. Nickel to the fore.
  Science, 293, 1264-1265.  
11489867 V.Svetlitchnyi, C.Peschel, G.Acker, and O.Meyer (2001).
Two membrane-associated NiFeS-carbon monoxide dehydrogenases from the anaerobic carbon-monoxide-utilizing eubacterium Carboxydothermus hydrogenoformans.
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11076017 J.Köhrl, R.Brigelius-Flohé, A.Böck, R.Gärtner, O.Meyer, and L.Flohé (2000).
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11054113 R.Bingemann, and A.Klein (2000).
Conversion of the central [4Fe-4S] cluster into a [3Fe-4S] cluster leads to reduced hydrogen-uptake activity of the F420-reducing hydrogenase of Methanococcus voltae.
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Structure and mechanism of iron-only hydrogenases.
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Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase.
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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.