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(-) Description

Title :  CRYSTAL STRUCTURE OF FE-HYDROGENASE FROM METHANOTHERMOBACTER MARBURGENSIS IN COMPLEX WITH 2-NAPHTHYLISOCYANIDE
 
Authors :  H. Tamura, E. Warkentin, U. Ermler, S. Shima
Date :  07 Mar 13  (Deposition) - 07 Aug 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Fold, Hydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tamura, M. Salomone-Stagni, T. Fujishiro, E. Warkentin, W. Meyer-Klaucke, U. Ermler, S. Shima
Crystal Structures Of [Fe]-Hydrogenase In Complex With Inhibitory Isocyanides: Implications For The H2 -Activation Site.
Angew. Chem. Int. Ed. Engl. V. 52 9656 2013
PubMed-ID: 23873755  |  Reference-DOI: 10.1002/ANIE.201305089

(-) Compounds

Molecule 1 - 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE
    Chains: A, B
    EC Number: 1.12.98.2
    Organism Scientific: METHANOTHERMOBACTER MARBURGENSIS
    Organism Taxid: 79929
    Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / MARBURG
    Synonym: H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE, H(2)-FORMING N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE, N(5), N(10)-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FE92Ligand/IonIRON-GUANYLYL PYRIDINOL COFACTOR
2N2I2Ligand/IonN-(NAPHTHALEN-2-YL)METHANIMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:6 , GLY A:7 , ALA A:8 , GLY A:9 , CYS A:10 , THR A:13 , ALA A:62 , ASP A:63 , PRO A:64 , PRO A:110 , PRO A:111 , ASP A:131 , TRP A:144 , PHE A:145 , PRO A:146 , ILE A:154 , ALA A:171 , CYS A:172 , PRO A:204 , ALA A:206 , VAL A:207 , PRO A:208 , N2I A:402 , HOH A:543 , HOH A:546BINDING SITE FOR RESIDUE FE9 A 401
2AC2SOFTWARECYS A:172 , GLY A:205 , CYS A:252 , FE9 A:401BINDING SITE FOR RESIDUE N2I A 402
3AC3SOFTWARELEU B:6 , GLY B:7 , GLY B:9 , CYS B:10 , THR B:13 , ALA B:62 , ASP B:63 , PRO B:64 , PRO B:110 , PRO B:111 , ASP B:131 , TRP B:144 , PHE B:145 , PRO B:146 , ILE B:154 , ALA B:171 , CYS B:172 , HIS B:203 , PRO B:204 , ALA B:206 , VAL B:207 , PRO B:208 , N2I B:402BINDING SITE FOR RESIDUE FE9 B 401
4AC4SOFTWARECYS B:172 , GLY B:205 , CYS B:252 , FE9 B:401BINDING SITE FOR RESIDUE N2I B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JJF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:110 -Pro A:111
2Pro B:110 -Pro B:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JJF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JJF)

(-) Exons   (0, 0)

(no "Exon" information available for 4JJF)

(-) Sequences/Alignments

Asymmetric/Biological 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
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jjfa1 A:1-244 automated matches                                                                                                                                                                                                                   d4jjfa2 A:245-344 automated matches                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhheeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh.eee.hhhhhhh...eeee.....hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh......hhhhheeee............eeeee...hhhhhhhhhhhhhhhhh.eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jjf A   1 MKLAILGAGCYRTHAASGITNFSRACEVAEMVGKPEIAMTHSTITMGAELKELAGVDEVVVADPVFDNQFTVIDDFAYEDVIEAHKEDPEKIMPQIREKVNEVAKELPKPPEGAIHFTHPEDLGFEITTDDREAVADADFIMTWFPKGDMQPDIINKFIDDIKPGAIVTHACTIPTTKFYKIFEQKHGDLVTKPETLNVTSYHPGAVPEMKGQVYIAEGYASEDAIETLFELGQKARGNAYRLPAELLGPVCDMCSALTAITYAGILSYRDSVTQVLGAPASFAQMMAKESLEQITALMEKVGIDKMEENLDPGALLGTADSMNFGASAEILPTVFEILEKRKK 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    


Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jjfb1 B:1-244 automated matches                                                                                                                                                                                                                   d4jjfb2 B:245-344 automated matches                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhheeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh.eee.hhhhhhh...eeee.....hhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......hhhhheeee............eeeee...hhhhhhhhhhhhhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jjf B   1 MKLAILGAGCYRTHAASGITNFSRACEVAEMVGKPEIAMTHSTITMGAELKELAGVDEVVVADPVFDNQFTVIDDFAYEDVIEAHKEDPEKIMPQIREKVNEVAKELPKPPEGAIHFTHPEDLGFEITTDDREAVADADFIMTWFPKGDMQPDIINKFIDDIKPGAIVTHACTIPTTKFYKIFEQKHGDLVTKPETLNVTSYHPGAVPEMKGQVYIAEGYASEDAIETLFELGQKARGNAYRLPAELLGPVCDMCSALTAITYAGILSYRDSVTQVLGAPASFAQMMAKESLEQITALMEKVGIDKMEENLDPGALLGTADSMNFGASAEILPTVFEILEKRKK 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)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JJF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JJF)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro A:110 - Pro A:111   [ RasMol ]  
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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_METTM | P32440: 4jjg

(-) Related Entries Specified in the PDB File

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3f47 HOLOENZYME FROM METHANOCALDOCOCCUS JANNASCHII