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(-) Description

Title :  HCGB FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH THE GUANYLYL-PYRIDINOL PRODUCT IN A MODEL REACTION OF [FE]-HYDROGENASE COFACTOR BIOSYNTHESIS
 
Authors :  T. Fujishiro, U. Ermler, S. Shima
Date :  11 May 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gtp-Binding Domain, Guanylyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fujishiro, H. Tamura, M. Schick, J. Kahnt, X. Xie, U. Ermler, S. Shim
Identification Of The Hcgb Enzyme In [Fe]-Hydrogenase-Cofactor Biosynthesis.
Angew. Chem. Int. Ed. Engl. V. 52 12555 2013
PubMed-ID: 24249552  |  Reference-DOI: 10.1002/ANIE.201306745

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0488
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-158
    Gene: HCGB, MJ0488
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3YGP4Ligand/Ion5'-O-[(R)-[(3,6-DIMETHYL-2-OXO-1,2-DIHYDROPYRIDIN-4-YL)OXY](HYDROXY)PHOSPHORYL]GUANOSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:20 , ARG A:21 , GLY A:22 , ASP A:23 , LYS B:50 , ASP B:77 , ARG B:102 , GLY B:103 , ARG B:104 , GLY B:111 , SER B:132 , HIS B:135 , GLU B:137 , ILE B:139 , HOH B:209 , HOH B:211BINDING SITE FOR RESIDUE YGP A 201
2AC2SOFTWARELYS A:50 , ASP A:77 , ARG A:102 , GLY A:103 , ARG A:104 , GLY A:111 , HIS A:135 , GLU A:137 , ARG A:142 , GDP A:204 , HOH A:328 , HOH A:333 , ARG B:20 , ARG B:21 , GLY B:22 , ASP B:23BINDING SITE FOR RESIDUE YGP A 202
3AC3SOFTWAREGDP A:204 , HOH A:326 , HOH A:327 , HOH A:328 , HOH A:334BINDING SITE FOR RESIDUE MG A 203
4AC4SOFTWAREASN A:17 , THR A:45 , ASN A:46 , ASN A:47 , LYS A:50 , THR A:73 , LYS A:86 , YGP A:202 , MG A:203 , HOH A:326 , HOH A:333 , ARG B:21BINDING SITE FOR RESIDUE GDP A 204
5AC5SOFTWAREGLU A:160 , HOH A:341 , HOH A:342 , GLU D:160BINDING SITE FOR RESIDUE MG A 205
6AC6SOFTWAREARG C:20 , ARG C:21 , GLY C:22 , ASP C:23 , HOH C:317 , LYS D:86 , ARG D:102 , ARG D:104 , GLY D:111 , SER D:132 , HIS D:135 , GLU D:137 , ILE D:139BINDING SITE FOR RESIDUE YGP C 201
7AC7SOFTWARELYS C:50 , ASP C:77 , ARG C:102 , ARG C:104 , GLY C:111 , SER C:132 , HIS C:135 , GLU C:137 , ARG C:142 , ARG D:20 , ARG D:21 , GLY D:22 , ASP D:23BINDING SITE FOR RESIDUE YGP C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WB2)

(-) Exons   (0, 0)

(no "Exon" information available for 3WB2)

(-) 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:160
 aligned with Y488_METJA | Q57912 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                                                                                                                                                                                      158   
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -
           Y488_METJA     2 IVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.....eeee....hhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee.hhhhhh.hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb2 A   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISILEH 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Y488_METJA | Q57912 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           Y488_METJA     2 IVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh.....eee....hhhhhh...hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee.hhhhhh.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb2 B   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Y488_METJA | Q57912 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           Y488_METJA     2 IVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh.....eeee...hhhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee.hhhhhh.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb2 C   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain D from PDB  Type:PROTEIN  Length:160
 aligned with Y488_METJA | Q57912 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:160
                                                                                                                                                                                      158   
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -
           Y488_METJA     2 IVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI---   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eeeee..hhhhh....hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee.hhhhhh.hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb2 D   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISILEH 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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  (0, 0)

(no "SCOP Domain" information available for 3WB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WB2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WB2)

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  Cis Peptide Bonds
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  3wb2
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  Y488_METJA | Q57912
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 Related Entries

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

UniProtKB/Swiss-Prot
        Y488_METJA | Q57912: 3wb0 3wb1 5d5q

(-) Related Entries Specified in the PDB File

3brc HCGB FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS
3wb0
3wb1