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PDBsum entry 1n62

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1n62
Jmol
Contents
Protein chains
161 a.a. *
804 a.a. *
286 a.a. *
Ligands
PO4
FES ×4
CUB-MCN ×2
FAD ×2
Waters ×3219
* Residue conservation analysis
PDB id:
1n62
Name: Oxidoreductase
Title: Crystal structure of the mo,cu-co dehydrogenase (codh), n- butylisocyanide-bound state
Structure: Carbon monoxide dehydrogenase small chain. Chain: a, d. Synonym: co dehydrogenase subunit s. Carbon monoxide dehydrogenase large chain. Chain: b, e. Synonym: co dehydrogenase subunit l. Carbon monoxide dehydrogenase medium chain. Chain: c, f. Synonym: co dehydrogenase subunit m.
Source: Oligotropha carboxidovorans. Organism_taxid: 504832. Strain: om5. Strain: om5
Biol. unit: Hexamer (from PQS)
Resolution:
1.09Å     R-factor:   0.144     R-free:   0.172
Authors: H.Dobbek,L.Gremer,R.Kiefersauer,R.Huber,O.Meyer
Key ref:
H.Dobbek et al. (2002). Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution. Proc Natl Acad Sci U S A, 99, 15971-15976. PubMed id: 12475995 DOI: 10.1073/pnas.212640899
Date:
08-Nov-02     Release date:   18-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19921  (DCMS_OLICO) -  Carbon monoxide dehydrogenase small chain
Seq:
Struc:
166 a.a.
161 a.a.
Protein chains
Pfam   ArchSchema ?
P19919  (DCML_OLICO) -  Carbon monoxide dehydrogenase large chain
Seq:
Struc:
 
Seq:
Struc:
809 a.a.
804 a.a.
Protein chains
Pfam   ArchSchema ?
P19920  (DCMM_OLICO) -  Carbon monoxide dehydrogenase medium chain
Seq:
Struc:
288 a.a.
286 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.1.2.99.2  - Carbon-monoxide dehydrogenase (acceptor).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: CO + H2O + A = CO2 + AH2
CO
+ H(2)O
+
= CO(2)
+ AH(2)
      Cofactor: Iron-sulfur; Ni(2+)
Iron-sulfur
Ni(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     12 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.212640899 Proc Natl Acad Sci U S A 99:15971-15976 (2002)
PubMed id: 12475995  
 
 
Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution.
H.Dobbek, L.Gremer, R.Kiefersauer, R.Huber, O.Meyer.
 
  ABSTRACT  
 
The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's active site in the oxidized or reduced state, after inactivation with potassium cyanide or with n-butylisocyanide bound to the active site, has been reinvestigated by multiple wavelength anomalous dispersion measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses. We present evidence cluster in the active site of the oxidized or reduced enzyme, which is prone to cyanolysis. The cluster is coordinated through interactions of the Mo with the dithiolate pyran ring of molybdopterin cytosine dinucleotide and of the Cu with the Sgamma of Cys-388, which is part of the active-site loop VAYRC(388)SFR. The previously reported active-site structure [Dobbek, H., Gremer, L., Meyer, O. & Huber, R. (1999) of an Mo with three oxygen ligands and an SeH-group bound to the Sgamma atom of Cys-388 could not be confirmed. The structure of CO dehydrogenase with the inhibitor n-butylisocyanide bound has led to a model for the catalytic mechanism of CO oxidation which involves a cluster of CO dehydrogenase establishes a previously uncharacterized class of dinuclear molybdoenzymes containing the pterin cofactor.
 
  Selected figure(s)  
 
Figure 1.
Fig 1. (A) UV/visible spectra of CODH after reduction with CO (I) or dithionite (II). (I) Curve a, air-oxidized; curve b, reduced with pure CO for 1, 15, 30, or 60 min, respectively. (Inset c) Difference spectrum of air-oxidized minus CO-reduced for 60 min. (II) Curve a, air-oxidized; curve b, reduced with 325 µM dithionite under an atmosphere of pure Ar for 4 min. The spectrum has been corrected with respect to the absorbance of unreacted dithionite. (Inset c) Difference spectrum of air-oxidized minus dithionite-reduced. CODH (4.8 µM) was in 50 mM Hepes buffer, pH 7.2. (B) Reactivity of CODH with potassium cyanide. CODH (10.8 µM in 50 mM Hepes buffer, pH 7.2; specific activity of 23.2 units/mg, set at 100%) was incubated with 5 mM potassium cyanide under an atmosphere of pure Ar. Samples were fractionated by ultrafiltration (30-kDa cutoff) into the protein fraction and the small molecule fraction. Cu was analyzed in both fractions by inductively coupled plasma atomic emission spectroscopy. Thiocyanate in the small molecule fraction was analyzed colorimetrically as Fe(SCN)[3] (31). The specific CO-oxidizing activities were determined in the protein fraction. (Inset) Epr spectra of CODH (36 µM) before (a) and after (b) inactivation with 5 mM potassium cyanide for 20 h. Samples were reduced with dithionite (4 mM) under an atmosphere of Ar, frozen in liquid nitrogen, and measured at 120 K (microwave frequency = 9.47 GHz, modulation amplitude = 1 mT, microwave power = 10 mW). (C) Analysis of the Cu in CODH by epr. a, Purified CODH. b, CODH after oxidative wet ashing with sulfuric acid/hydrogen peroxide. c, Protein fraction obtained by ultrafiltration of CODH treated with potassium cyanide. d, Same as c, but after oxidative wet ashing. e, Small molecule fraction obtained by ultrafiltration of CODH treated with potassium cyanide. f, Same as e, but after oxidative wet ashing. Epr spectra were recorded at 50 K (microwave frequency = 9.47 GHz, modulation amplitude = 1 mT, microwave power = 10 mW). (D) Stereo view of the [CuSMo( O)OH] cluster in the active site of CODH. The active site is built up by the bimetallic [CuSMo( O)OH] cluster in which the two metals are bridged by a µ-sulfido ligand. At the Mo site, the cluster is coordinated by the enedithiolate group of MCD. At the Cu site, the cluster is held by the S of Cys-388. The Mo also carries an apical oxo-group and an equatorial O-atom at a distance of 1.87 Å, which has been modeled as a hydroxo-group, although it is likely that the enzyme in solution carries an oxo-group at this position (11). Glu-763 interacts through its carboxyl atom (O 2) with the Mo ion in trans position to the oxo-group and is linked through hydrogen bonds to the active-site loop carrying Cys-388. Figs. 1D and 2 A-D were created with BOBSCRIPT (32) and RASTER 3D (33). (E) Inactivation of CODH by n-butylisocyanide. (I) Effect of the oxidation state of CODH (oxidized, dithionite-reduced, CO-reduced) on the inactivation with 1 mM n-butylisocyanide. (II) Specific requirement of the isocyanide group for the inactivation of CODH. The specific CODH activity was determined in the presence of 0.1 µM to 10 mM n-butylisocyanide, n-butanol, or n-butylcyanide, respectively. For experimental details, see Materials and Methods.
Figure 2.
Fig 2. Geometry of the bimetallic active site at different states. (A) The oxidized [CuSMo( O)OH] site. Additional distances: Cu-Mo, 3.74 Å; hydroxo-Cu, 3.36 Å; Cu-N (Cys-388), 3.14 Å; S8-S7, 3.15 Å; hydroxo-µS, 3.08 Å; hydroxo-O 2 (Glu-763), 2.99 Å; Mo-S (Cys-388), 5.91 Å. Angles of interest are: hydroxo-Mo-Oxo, 106°; oxo-Mo-µS, 107°; hydroxo-Mo-µS, 96°; Mo-µS-Cu, 113°; µS-Cu-S (Cys-388), 156°; oxo-Mo-S8, 101°; oxo-Mo-S7, 102°; S8-Mo-S7, 79°. (B) The cyanide-inactivated [MoO[3]] site. Additional distances: hydroxo-hydroxo, 2.71 Å; S8-S7, 3.12 Å; hydroxo-O 2 (Glu-763), 2.85 Å; Mo-S (Cys-388), 6.61 Å. Angles of interest are: hydroxo-Mo-oxo, 110°; hydroxo-Mo-hydroxo, 97°. (C) The reduced [CuSMo( O)OH] site. The geometry of the reduced site was the same irrespective of whether CO, H[2], or dithionite was used as a reductant. Additional distances: hydroxo-Cu, 3.32 Å; Cu-N (Cys-388), 3.10 Å; S8-S7, 3.14 Å; hydroxo-µS, 2.96 Å; hydroxo-O [2] (Glu-763), 2.77 Å; Mo-S (Cys-388), 6.05 Å. Angles of interest are: hydroxo Mo-Oxo, 109°; Oxo-Mo-µS, 107°; hydroxo Mo-S, 86°; Mo-µS-Cu, 122°; µS-Cu-S (Cys-388), 160°; oxo-Mo-S8, 104°; oxo-Mo-S7, 106°; S8-Mo-S7, 82°. (D) The n-butylisocyanide-containing site (stereo view). Additional distances: hydroxo-Cu, 3.90 Å; Cu-N (Cys-388), 3.33 Å; S8-S7, 3.08 Å; hydroxo-µS, 2.48 Å; hydroxo-O 2 (Glu-763), 3.01 Å; Mo-C, 2.63 Å; Mo-S (Cys-388), 6.84 Å; Mo-Cu, 5.07 Å. Angles of interest are: hydroxo-Mo-oxo, 105°; oxo-Mo-µS, 113°; hydroxo-Mo-S, 69°; Mo-µS-Cu, 135°; N (nBIC)-Cu-S (Cys-388), 169°; oxo-Mo-S8, 105°; oxo-Mo-S7, 105°; S8-Mo-S7, 83°. Map coefficients and contour levels are given in parentheses. ( [A] weighted 2F[obs]-F[calc]. Lines at 1.0 and surface at 2.5 contoured.) The indicated distances and angles are average values between the two monomers found per asymmetric unit, respectively, in the two high resolution structures in the reduced state. Distances are given in Å. (E) Hypothetical scheme showing the oxidation of CO to CO[2] at the [CuSMo( O)OH] site of CODH. The catalytic cycle starts at the oxidized [CuSMo( O)OH] cluster with the integration of the CO between the Cu ion and the S- and the equatorial O-ligand of the Mo. The intermediate state shown is hypothetical because its structure has been deduced from the crystal structure of the n-butylisocyanide-bound state (D). All other states shown are based on their individual crystal structures (A and C). In the Transition state, the CO undergoes a nucleophilic attack by the equatorial O with the formation of a thiocarbonate intermediate and reduction of the Mo ion from the +VI to the +IV state. The thiocarbonate then breaks down to CO[2], and the equatorial hydroxo group is regenerated from water, yielding the reduced state of the cluster. Finally, the Mo(+IV) is reoxidized to Mo(+VI) through the transfer of the electrons via FeS I into the intramolecular electron transport, which completes the reaction cycle.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21301738 A.Beheshti, W.Clegg, R.Khorramdin, V.Nobakht, and L.Russo (2011).
Synthesis and structural characterization of mixed-metal complexes of Cu(I) with MOS3 cores (M = Mo, W) and of an unusual polymeric AgI/mercaptoimidazole complex with five different Ag(I) coordination environments.
  Dalton Trans, 40, 2815-2821.  
  21151514 M.Neumann, and S.Leimkühler (2011).
The role of system-specific molecular chaperones in the maturation of molybdoenzymes in bacteria.
  Biochem Res Int, 2011, 850924.  
21186382 P.V.Bernhardt (2011).
Exploiting the versatility and selectivity of Mo enzymes with electrochemistry.
  Chem Commun (Camb), 47, 1663-1673.  
19965379 H.M.Alvarez, Y.Xue, C.D.Robinson, M.A.Canalizo-Hernández, R.G.Marvin, R.A.Kelly, A.Mondragón, J.E.Penner-Hahn, and T.V.O'Halloran (2010).
Tetrathiomolybdate inhibits copper trafficking proteins through metal cluster formation.
  Science, 327, 331-334.
PDB code: 3k7r
20616070 M.Köpke, C.Held, S.Hujer, H.Liesegang, A.Wiezer, A.Wollherr, A.Ehrenreich, W.Liebl, G.Gottschalk, and P.Dürre (2010).
Clostridium ljungdahlii represents a microbial production platform based on syngas.
  Proc Natl Acad Sci U S A, 107, 13087-13092.  
19189964 A.Pelzmann, M.Ferner, M.Gnida, W.Meyer-Klaucke, T.Maisel, and O.Meyer (2009).
The CoxD protein of Oligotropha carboxidovorans is a predicted AAA+ ATPase chaperone involved in the biogenesis of the CO dehydrogenase [CuSMoO2] cluster.
  J Biol Chem, 284, 9578-9586.  
19088968 E.E.Benson, C.P.Kubiak, A.J.Sathrum, and J.M.Smieja (2009).
Electrocatalytic and homogeneous approaches to conversion of CO(2) to liquid fuels.
  Chem Soc Rev, 38, 89-99.  
19675644 G.Schwarz, R.R.Mendel, and M.W.Ribbe (2009).
Molybdenum cofactors, enzymes and pathways.
  Nature, 460, 839-847.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19368556 M.Neumann, G.Mittelstädt, C.Iobbi-Nivol, M.Saggu, F.Lendzian, P.Hildebrandt, and S.Leimkühler (2009).
A periplasmic aldehyde oxidoreductase represents the first molybdopterin cytosine dinucleotide cofactor containing molybdo-flavoenzyme from Escherichia coli.
  FEBS J, 276, 2762-2774.  
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.  
19319403 Z.G.Ren, J.Y.Yang, Y.L.Song, N.Y.Li, H.X.Li, Y.Chen, Y.Zhang, and J.P.Lang (2009).
From trans-[(eta5-C5Me5)2Mo2S2(mu-S)2] to [(eta5-C5Me5)2Mo2(mu3-S)4(CuMeCN)2]2+ to [(eta5-C5Me5)2Mo2(mu3-S)4Cu2]-based polymeric and dimeric clusters: syntheses, structures and enhanced third-order non-linear optical performances.
  Dalton Trans, (), 2578-2587.  
18575848 E.Oelgeschläger, and M.Rother (2008).
Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea.
  Arch Microbiol, 190, 257-269.  
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.  
17139522 A.Thapper, D.R.Boer, C.D.Brondino, J.J.Moura, and M.J.Romão (2007).
Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.
  J Biol Inorg Chem, 12, 353-366.
PDB code: 3l4p
17687573 M.S.Morrison, P.A.Cobine, and E.L.Hegg (2007).
Probing the role of copper in the biosynthesis of the molybdenum cofactor in Escherichia coli and Rhodobacter sphaeroides.
  J Biol Inorg Chem, 12, 1129-1139.  
17716738 S.W.Ragsdale (2007).
Nickel and the carbon cycle.
  J Inorg Biochem, 101, 1657-1666.  
16480912 C.D.Brondino, M.J.Romão, I.Moura, and J.J.Moura (2006).
Molybdenum and tungsten enzymes: the xanthine oxidase family.
  Curr Opin Chem Biol, 10, 109-114.  
16385608 M.E.Helton, D.Maiti, L.N.Zakharov, A.L.Rheingold, J.A.Porco, and K.D.Karlin (2006).
A mu-eta2:eta2-disulfide dicopper(II) complex from reaction of S8 with a copper(I) precursor: reactivity of the bound disulfur moiety.
  Angew Chem Int Ed Engl, 45, 1138-1141.  
16820521 P.Sachelaru, E.Schiltz, and R.Brandsch (2006).
A functional mobA gene for molybdopterin cytosine dinucleotide cofactor biosynthesis is required for activity and holoenzyme assembly of the heterotrimeric nicotine dehydrogenases of Arthrobacter nicotinovorans.
  Appl Environ Microbiol, 72, 5126-5131.  
16234923 A.Volbeda, and J.C.Fontecilla-Camps (2005).
Structural bases for the catalytic mechanism of Ni-containing carbon monoxide dehydrogenases.
  Dalton Trans, (), 3443-3450.  
15651045 D.Fenske, M.Gnida, K.Schneider, W.Meyer-Klaucke, J.Schemberg, V.Henschel, A.K.Meyer, A.Knöchel, and A.Müller (2005).
A new type of metalloprotein: The Mo storage protein from azotobacter vinelandii contains a polynuclear molybdenum-oxide cluster.
  Chembiochem, 6, 405-413.  
  16508115 D.R.Boer, A.Müller, S.Fetzner, D.J.Lowe, and M.J.Romão (2005).
On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 137-140.  
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
15858259 M.E.Than, S.Henrich, G.P.Bourenkov, H.D.Bartunik, R.Huber, and W.Bode (2005).
The endoproteinase furin contains two essential Ca2+ ions stabilizing its N-terminus and the unique S1 specificity pocket.
  Acta Crystallogr D Biol Crystallogr, 61, 505-512.  
15971074 M.Hofmann, J.K.Kassube, and T.Graf (2005).
The mechanism of Mo-/Cu-dependent CO dehydrogenase.
  J Biol Inorg Chem, 10, 490-495.  
16091936 M.Resch, H.Dobbek, and O.Meyer (2005).
Structural and functional reconstruction in situ of the [CuSMoO2] active site of carbon monoxide dehydrogenase from the carbon monoxide oxidizing eubacterium Oligotropha carboxidovorans.
  J Biol Inorg Chem, 10, 518-528.
PDB code: 1zxi
15834924 P.E.Siegbahn, and A.F.Shestakov (2005).
Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase.
  J Comput Chem, 26, 888-898.  
15901710 S.L.Andrade, F.Cruz, C.L.Drennan, V.Ramakrishnan, D.C.Rees, J.G.Ferry, and O.Einsle (2005).
Structures of the iron-sulfur flavoproteins from Methanosarcina thermophila and Archaeoglobus fulgidus.
  J Bacteriol, 187, 3848-3854.  
15353565 G.P.Roberts, H.Youn, and R.L.Kerby (2004).
CO-sensing mechanisms.
  Microbiol Mol Biol Rev, 68, 453-473.  
15296736 I.Bonin, B.M.Martins, V.Purvanov, S.Fetzner, R.Huber, and H.Dobbek (2004).
Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase.
  Structure, 12, 1425-1435.
PDB code: 1t3q
15148401 K.Okamoto, K.Matsumoto, R.Hille, B.T.Eger, E.F.Pai, and T.Nishino (2004).
The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition.
  Proc Natl Acad Sci U S A, 101, 7931-7936.
PDB code: 1v97
15576037 M.Unciuleac, E.Warkentin, C.C.Page, M.Boll, and U.Ermler (2004).
Structure of a xanthine oxidase-related 4-hydroxybenzoyl-CoA reductase with an additional [4Fe-4S] cluster and an inverted electron flow.
  Structure, 12, 2249-2256.
PDB codes: 1rm6 1sb3
12654012 U.Frerichs-Deeken, B.Goldenstedt, R.Gahl-Janssen, R.Kappl, J.Hüttermann, and S.Fetzner (2003).
Functional expression of the quinoline 2-oxidoreductase genes (qorMSL) in Pseudomonas putida KT2440 pUF1 and in P. putida 86-1 deltaqor pUF1 and analysis of the Qor proteins.
  Eur J Biochem, 270, 1567-1577.  
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.