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PDBsum entry 1aa6

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protein ligands metals links
Oxidoreductase PDB id
1aa6
Jmol
Contents
Protein chain
697 a.a. *
Ligands
SF4
MGD ×2
Metals
4MO
Waters ×83
* Residue conservation analysis
PDB id:
1aa6
Name: Oxidoreductase
Title: Reduced form of formate dehydrogenase h from e. Coli
Structure: Formate dehydrogenase h. Chain: a. Synonym: fdh-h. Engineered: yes. Other_details: reduced form (mo(iv),fe4s4(red)) of fdh-h
Source: Escherichia coli. Organism_taxid: 562. Strain: fm911. Gene: fdhf. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: fdh-h was expressed anaerobically
Resolution:
2.30Å     R-factor:   0.217     R-free:   0.287
Authors: P.D.Sun,J.C.Boyington
Key ref:
J.C.Boyington et al. (1997). Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science, 275, 1305-1308. PubMed id: 9036855 DOI: 10.1126/science.275.5304.1305
Date:
23-Jan-97     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07658  (FDHF_ECOLI) -  Formate dehydrogenase H
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)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     electron carrier activity     7 terms  

 

 
DOI no: 10.1126/science.275.5304.1305 Science 275:1305-1308 (1997)
PubMed id: 9036855  
 
 
Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.
J.C.Boyington, V.N.Gladyshev, S.V.Khangulov, T.C.Stadtman, P.D.Sun.
 
  ABSTRACT  
 
Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Schematic representation of the hydrogen-bonding network coordinating MGD^801 and MGD^802. Residues are color-coded according to sequence conservation^ among the known sequences of MGD-containing FDH enzymes (11):^ magenta, invariant; blue, well conserved; and green, not conserved.^ The eight water molecules involved in hydrogen-bonding interactions^ are designated by orange circles. Hydrogen bonds present in the^ oxidized state, the reduced state, or both states are represented^ by blue, red, or black dashed lines, respectively.
Figure 5.
Fig. 5. The proposed reaction mechanism for FDH[H]. BV, benzyl viologen.
 
  The above figures are reprinted by permission from the AAAs: Science (1997, 275, 1305-1308) copyright 1997.  
  Figures were selected by an automated process.  

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.
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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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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 (dagger).
  Biochemistry, 48, 2310-2320.  
19201964 Z.Waks, and P.A.Silver (2009).
Engineering a synthetic dual-organism system for hydrogen production.
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19020675 H.Sugimoto, and H.Tsukube (2008).
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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.  
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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18801467 S.W.Ragsdale, and E.Pierce (2008).
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.
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18335216 T.Maeda, V.Sanchez-Torres, and T.K.Wood (2008).
Protein engineering of hydrogenase 3 to enhance hydrogen production.
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18667702 T.Reda, C.M.Plugge, N.J.Abram, and J.Hirst (2008).
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme.
  Proc Natl Acad Sci U S A, 105, 10654-10658.  
18485362 Y.Zhang, and V.N.Gladyshev (2008).
Molybdoproteomes and evolution of molybdenum utilization.
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18021072 E.V.Morozkina, and R.A.Zvyagilskaya (2007).
Nitrate reductases: structure, functions, and effect of stress factors.
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17360611 G.B.Seiffert, G.M.Ullmann, A.Messerschmidt, B.Schink, P.M.Kroneck, and O.Einsle (2007).
Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.
  Proc Natl Acad Sci U S A, 104, 3073-3077.
PDB code: 2e7z
17456740 J.A.Knappenberger, and J.T.Lecomte (2007).
Loop anchor modification causes the population of an alternative native state in an SH3-like domain.
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17600788 K.Pal, P.K.Chaudhury, and S.Sarkar (2007).
Structure of the Michaelis complex and function of the catalytic center in the reductive half-reaction of computational and synthetic models of sulfite oxidase.
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17937613 L.A.Wessjohann, A.Schneider, M.Abbas, and W.Brandt (2007).
Selenium in chemistry and biochemistry in comparison to sulfur.
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17704896 M.J.Russell (2007).
The alkaline solution to the emergence of life: energy, entropy and early evolution.
  Acta Biotheor, 55, 133-179.  
17277802 T.L.Hendrickson (2007).
Easing selenocysteine into proteins.
  Nat Struct Mol Biol, 14, 100-101.  
17255002 W.Martin, and M.J.Russell (2007).
On the origin of biochemistry at an alkaline hydrothermal vent.
  Philos Trans R Soc Lond B Biol Sci, 362, 1887-1925.  
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.  
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
16640566 J.Weiner, F.Beaussart, and E.Bornberg-Bauer (2006).
Domain deletions and substitutions in the modular protein evolution.
  FEBS J, 273, 2037-2047.  
16411255 M.Leopoldini, N.Russo, M.Toscano, M.Dulak, and T.A.Wesolowski (2006).
Mechanism of nitrate reduction by Desulfovibrio desulfuricans nitrate reductase--a theoretical investigation.
  Chemistry, 12, 2532-2541.  
16385560 Y.Kim, and S.Subramaniam (2006).
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships.
  Proteins, 62, 1115-1124.  
16269707 A.Yoshida, T.Nishimura, H.Kawaguchi, M.Inui, and H.Yukawa (2005).
Enhanced hydrogen production from formic acid by formate hydrogen lyase-overexpressing Escherichia coli strains.
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15702182 C.Schulzke (2005).
Temperature dependent electrochemical investigations of molybdenum and tungsten oxobisdithiolene complexes.
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15665870 S.Yoshizawa, L.Rasubala, T.Ose, D.Kohda, D.Fourmy, and K.Maenaka (2005).
Structural basis for mRNA recognition by elongation factor SelB.
  Nat Struct Mol Biol, 12, 198-203.
PDB code: 1wsu
15284442 A.Messerschmidt, H.Niessen, D.Abt, O.Einsle, B.Schink, and P.M.Kroneck (2004).
Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols.
  Proc Natl Acad Sci U S A, 101, 11571-11576.
PDB codes: 1ti2 1ti4 1ti6 1vld 1vle 1vlf
15028701 F.Peters, M.Rother, and M.Boll (2004).
Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans.
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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.
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14711625 R.S.Oremland, M.J.Herbel, J.S.Blum, S.Langley, T.J.Beveridge, P.M.Ajayan, T.Sutto, A.V.Ellis, and S.Curran (2004).
Structural and spectral features of selenium nanospheres produced by Se-respiring bacteria.
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15486691 T.Tomiki, and N.Saitou (2004).
Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration.
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14563877 C.Merlin, M.Masters, S.McAteer, and A.Coulson (2003).
Why is carbonic anhydrase essential to Escherichia coli?
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12755703 F.A.de Bok, P.L.Hagedoorn, P.J.Silva, W.R.Hagen, E.Schiltz, K.Fritsche, and A.J.Stams (2003).
Two W-containing formate dehydrogenases (CO2-reductases) involved in syntrophic propionate oxidation by Syntrophobacter fumaroxidans.
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12910261 M.G.Bertero, R.A.Rothery, M.Palak, C.Hou, D.Lim, F.Blasco, J.H.Weiner, and N.C.Strynadka (2003).
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
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PDB code: 1q16
12948771 M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
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12605683 M.Laukel, L.Chistoserdova, M.E.Lidstrom, and J.A.Vorholt (2003).
The tungsten-containing formate dehydrogenase from Methylobacterium extorquens AM1: purification and properties.
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12067345 C.A.McDevitt, P.Hugenholtz, G.R.Hanson, and A.G.McEwan (2002).
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.
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12220497 H.Raaijmakers, S.Macieira, J.M.Dias, S.Teixeira, S.Bursakov, R.Huber, J.J.Moura, I.Moura, and M.J.Romão (2002).
Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
  Structure, 10, 1261-1272.
PDB code: 1h0h
12165429 J.Simon (2002).
Enzymology and bioenergetics of respiratory nitrite ammonification.
  FEMS Microbiol Rev, 26, 285-309.  
11929547 N.R.Stanley, F.Sargent, G.Buchanan, J.Shi, V.Stewart, T.Palmer, and B.C.Berks (2002).
Behaviour of topological marker proteins targeted to the Tat protein transport pathway.
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12114025 R.Hille (2002).
Molybdenum and tungsten in biology.
  Trends Biochem Sci, 27, 360-367.  
12045088 T.C.Stadtman, and T.C.Stadtman (2002).
Discoveries of vitamin B12 and selenium enzymes.
  Annu Rev Biochem, 71, 1.  
11889113 W.T.Self (2002).
Regulation of purine hydroxylase and xanthine dehydrogenase from Clostridium purinolyticum in response to purines, selenium, and molybdenum.
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12398720 X.Yang, X.B.Wang, S.Niu, C.J.Pickett, T.Ichiye, and L.S.Wang (2002).
Coulomb- and antiferromagnetic-induced fission in doubly charged cubelike fe-s clusters.
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11532013 B.K.Pomper, and J.A.Vorholt (2001).
Characterization of the formyltransferase from Methylobacterium extorquens AM1.
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11717511 D.Pignol, J.M.Adriano, J.C.Fontecilla-Camps, and M.Sabaty (2001).
Crystallization and preliminary X-ray analysis of the periplasmic nitrate reductase (NapA-NapB complex) from Rhodobacter sphaeroides f. sp. denitrificans.
  Acta Crystallogr D Biol Crystallogr, 57, 1900-1902.  
11443080 F.Kaufmann, and D.R.Lovley (2001).
Isolation and characterization of a soluble NADPH-dependent Fe(III) reductase from Geobacter sulfurreducens.
  J Bacteriol, 183, 4468-4476.  
11443088 H.A.Johnson, D.A.Pelletier, and A.M.Spormann (2001).
Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme.
  J Bacteriol, 183, 4536-4542.  
11743004 J.B.Mansell, D.Guévremont, E.S.Poole, and W.P.Tate (2001).
A dynamic competition between release factor 2 and the tRNA(Sec) decoding UGA at the recoding site of Escherichia coli formate dehydrogenase H.
  EMBO J, 20, 7284-7293.  
11250197 P.J.Ellis, T.Conrads, R.Hille, and P.Kuhn (2001).
Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
  Structure, 9, 125-132.
PDB codes: 1g8j 1g8k
11481439 T.Sandalova, L.Zhong, Y.Lindqvist, A.Holmgren, and G.Schneider (2001).
Three-dimensional structure of a mammalian thioredoxin reductase: implications for mechanism and evolution of a selenocysteine-dependent enzyme.
  Proc Natl Acad Sci U S A, 98, 9533-9538.
PDB code: 1h6v
10747793 C.A.Temple, G.N.George, J.C.Hilton, M.J.George, R.C.Prince, M.J.Barber, and K.V.Rajagopalan (2000).
Structure of the molybdenum site of Rhodobacter sphaeroides biotin sulfoxide reductase.
  Biochemistry, 39, 4046-4052.  
11076017 J.Köhrl, R.Brigelius-Flohé, A.Böck, R.Gärtner, O.Meyer, and L.Flohé (2000).
Selenium in biology: facts and medical perspectives.
  Biol Chem, 381, 849-864.  
11076018 O.Meyer, L.Gremer, R.Ferner, M.Ferner, H.Dobbek, M.Gnida, W.Meyer-Klaucke, and R.Huber (2000).
The role of Se, Mo and Fe in the structure and function of carbon monoxide dehydrogenase.
  Biol Chem, 381, 865-876.  
  10689164 W.T.Self, and K.T.Shanmugam (2000).
Isolation and characterization of mutated FhlA proteins which activate transcription of the hyc operon (formate hydrogenlyase) of Escherichia coli in the absence of molybdate(1).
  FEMS Microbiol Lett, 184, 47-52.  
10387097 B.Adams, A.T.Smith, S.Bailey, A.G.McEwan, and R.C.Bray (1999).
Reactions of dimethylsulfoxide reductase from Rhodobacter capsulatus with dimethyl sulfide and with dimethyl sulfoxide: complexities revealed by conventional and stopped-flow spectrophotometry.
  Biochemistry, 38, 8501-8511.  
10413473 C.S.Butler, J.M.Charnock, B.Bennett, H.J.Sears, A.J.Reilly, S.J.Ferguson, C.D.Garner, D.J.Lowe, A.J.Thomson, B.C.Berks, and D.J.Richardson (1999).
Models for molybdenum coordination during the catalytic cycle of periplasmic nitrate reductase from Paracoccus denitrificans derived from EPR and EXAFS spectroscopy.
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10348621 D.J.Richardson, and N.J.Watmough (1999).
Inorganic nitrogen metabolism in bacteria.
  Curr Opin Chem Biol, 3, 207-219.  
10378275 E.Garcin, X.Vernede, E.C.Hatchikian, A.Volbeda, M.Frey, and J.C.Fontecilla-Camps (1999).
The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
  Structure, 7, 557-566.
PDB code: 1cc1
10564479 J.I.Oh, and B.Bowien (1999).
Dual control by regulatory gene fdsR of the fds operon encoding the NAD+-linked formate dehydrogenase of Ralstonia eutropha.
  Mol Microbiol, 34, 365-376.  
10368307 J.M.Dias, M.E.Than, A.Humm, R.Huber, G.P.Bourenkov, H.D.Bartunik, S.Bursakov, J.Calvete, J.Caldeira, C.Carneiro, J.J.Moura, I.Moura, and M.J.Romão (1999).
Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.
  Structure, 7, 65-79.
PDB code: 2nap
10053004 J.Reiss, C.Dorche, B.Stallmeyer, R.R.Mendel, N.Cohen, and M.T.Zabot (1999).
Human molybdopterin synthase gene: genomic structure and mutations in molybdenum cofactor deficiency type B.
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10231485 M.Hensel, A.P.Hinsley, T.Nikolaus, G.Sawers, and B.C.Berks (1999).
The genetic basis of tetrathionate respiration in Salmonella typhimurium.
  Mol Microbiol, 32, 275-287.  
10587462 M.J.Almendra, C.D.Brondino, O.Gavel, A.S.Pereira, P.Tavares, S.Bursakov, R.Duarte, J.Caldeira, J.J.Moura, and I.Moura (1999).
Purification and characterization of a tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
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10368289 R.M.Castillo, K.Mizuguchi, V.Dhanaraj, A.Albert, T.L.Blundell, and A.G.Murzin (1999).
A six-stranded double-psi beta barrel is shared by several protein superfamilies.
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10447686 R.U.Meckenstock, R.Krieger, S.Ensign, P.M.Kroneck, and B.Schink (1999).
Acetylene hydratase of Pelobacter acetylenicus. Molecular and spectroscopic properties of the tungsten iron-sulfur enzyme.
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10491134 T.Schräder, A.Rienhöfer, and J.R.Andreesen (1999).
Selenium-containing xanthine dehydrogenase from Eubacterium barkeri.
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10343164 V.N.Gladyshev, and D.L.Hatfield (1999).
Selenocysteine-containing proteins in mammals.
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Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: investigation by site-directed mutagenesis of the conserved his-50 residue in the NarG subunit.
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Molybdopterin radical in bacterial aldehyde dehydrogenases.
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NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli.
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An edge with XAS.
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Mechanistic aspects of molybdenum-containing enzymes.
  FEMS Microbiol Rev, 22, 489-501.  
  9852007 S.Benoit, H.Abaibou, and M.A.Mandrand-Berthelot (1998).
Topological analysis of the aerobic membrane-bound formate dehydrogenase of Escherichia coli.
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9521673 S.V.Khangulov, V.N.Gladyshev, G.C.Dismukes, and T.C.Stadtman (1998).
Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer.
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9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
  Curr Opin Struct Biol, 8, 749-758.  
10099429 W.Neuhauser, M.Steininger, D.Haltrich, K.D.Kulbe, and B.Nidetzky (1998).
A pH-controlled fed-batch process can overcome inhibition by formate in NADH-dependent enzymatic reductions using formate dehydrogenase-catalyzed coenzyme regeneration.
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9428520 C.Kisker, H.Schindelin, A.Pacheco, W.A.Wehbi, R.M.Garrett, K.V.Rajagopalan, J.H.Enemark, and D.C.Rees (1997).
Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.
  Cell, 91, 973-983.
PDB code: 1sox
9342247 J.A.Vorholt, and R.K.Thauer (1997).
The active species of 'CO2' utilized by formylmethanofuran dehydrogenase from methanogenic Archaea.
  Eur J Biochem, 248, 919-924.  
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.