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(-) Description

Title :  THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE HOLOENZYME (HMD) FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  O. Pilak, E. Warkentin, S. Shima, R. K. Thauer, U. Ermler
Date :  29 May 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Helix Bundle, Methanogenesis, One-Carbon Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shima, O. Pilak, S. Vogt, M. Schick, M. S. Stagni, W. Meyer-Klaucke, E. Warkentin, R. K. Thauer, U. Ermler
The Crystal Structure Of [Fe]-Hydrogenase Reveals The Geometry Of The Active Site.
Science V. 321 572 2008
PubMed-ID: 18653896  |  Reference-DOI: 10.1126/SCIENCE.1158978

(-) Compounds

Molecule 1 - 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE
    Chains: A
    EC Number: 1.12.98.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24B
    Expression System Strain: B834 (DE3)(PLYSS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HMD, MJ0784
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Strain: DSMZ2661
    Synonym: H(2)-FORMING N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE, N(5),N(10)-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE, H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2FE21Ligand/IonFE (II) ION
3FEG1Ligand/Ion5'-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1CMO4Ligand/IonCARBON MONOXIDE
2FE22Ligand/IonFE (II) ION
3FEG2Ligand/Ion5'-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:6 , GLY A:7 , ALA A:8 , GLY A:9 , CYS A:10 , THR A:13 , HIS A:14 , SER A:63 , ASP A:64 , PRO A:65 , PRO A:114 , PRO A:115 , CYS A:118 , ASP A:135 , TRP A:148 , LEU A:149 , PRO A:150 , ILE A:158 , ALA A:175 , CYS A:176 , THR A:177 , HIS A:201 , PRO A:202 , CYS A:204 , PRO A:206BINDING SITE FOR RESIDUE FEG A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DAG)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:70 -Pro A:71
2Pro A:114 -Pro A:115
3Lys A:151 -Gly A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DAG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DAG)

(-) Exons   (0, 0)

(no "Exon" information available for 3DAG)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:344
 aligned with HMD_METJA | Q58194 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
            HMD_METJA     1 MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAELLHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKIREVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSYHPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEKHKVVE 344
               SCOP domains d3daga1 A:1-242 5,10-methenyltetrahydromethanopterin hydrogenase, HMD                                                                                                                                                                             d3daga2 A:243-344 5,10-methenyltetrahydromethanopterin hydrogenase, HMD                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh..eeee....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeee..hhhhhh.eee.hhhhhhh...eeee......hhhhhhhhhhhhh....eeee....hhhhhhhhhhhh.....eeee............eeeee...hhhhhhhhhhhhhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dag A   1 MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAELLHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKIREVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSYHPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEVHKVVE 344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DAG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DAG)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (HMD_METJA | Q58194)
molecular function
    GO:0047068    N5,N10-methenyltetrahydromethanopterin hydrogenase activity    Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2) = 5,10-methylenetetrahydromethanopterin + H(+).
    GO:0018537    coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity    Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0015948    methanogenesis    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    GO:0019386    methanogenesis, from carbon dioxide    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  HMD_METJA | Q58194
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  1.12.98.2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HMD_METJA | Q58194: 2b0j 3daf 3f46 3f47 3h65

(-) Related Entries Specified in the PDB File

2boj APOENZYME
3daf THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE HOLOENZYME (HMD) FROM METHANOCALDOCOCCUS JANNASCHII COCRYSTALLIZED WITH CYANIDE
3f46 C176A-MUTATED HOLOENZYME
3f47 RE-INTERPRETATION OF THE IRON-LIGAND STRUCTURE OF [FE]- HYDROGENASE HOLOENZYME (HMD) FROM METHANOCALDOCOCCUS JANNASCHII