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(-) Description

Title :  HCGB FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  H. Tamura, T. Fujishiro, U. Ermler, S. Shima
Date :  11 May 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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  (1, 19)

Asymmetric/Biological Unit (1, 19)
No.NameCountTypeFull Name
1SO419Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:3 , MET A:4 , LYS A:30 , LYS A:34 , LYS D:95BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWARETHR A:45 , ASN A:46 , ASN A:47 , LYS A:50 , LYS A:86 , SO4 A:203BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWARELYS A:50 , LYS A:86 , ARG A:102 , SER A:112 , SO4 A:202 , HOH A:308 , HOH A:319BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARELYS A:24 , GLU A:25 , HOH A:316BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREVAL B:3 , MET B:4 , GLU B:5 , LYS B:30 , LYS B:34 , LYS C:95BINDING SITE FOR RESIDUE SO4 B 201
06AC6SOFTWARELYS B:50 , LYS B:86 , ARG B:102 , GLY B:103 , SO4 B:203BINDING SITE FOR RESIDUE SO4 B 202
07AC7SOFTWARETHR B:45 , ASN B:46 , ASN B:47 , THR B:73 , LYS B:86 , SO4 B:202BINDING SITE FOR RESIDUE SO4 B 203
08AC8SOFTWAREGLY A:22 , ASP A:23 , SER B:112 , SER B:131 , SER B:132 , ARG B:142BINDING SITE FOR RESIDUE SO4 B 204
09AC9SOFTWARELEU A:88 , GLY A:121 , ARG B:80BINDING SITE FOR RESIDUE SO4 B 205
10BC1SOFTWARELYS B:24 , GLU B:25BINDING SITE FOR RESIDUE SO4 B 206
11BC2SOFTWAREVAL C:3 , MET C:4 , GLU C:5 , LYS C:30 , LYS C:34BINDING SITE FOR RESIDUE SO4 C 201
12BC3SOFTWARELYS C:50 , LYS C:86 , ARG C:102 , GLY C:103 , SO4 C:203BINDING SITE FOR RESIDUE SO4 C 202
13BC4SOFTWARETHR C:45 , ASN C:46 , ASN C:47 , LYS C:50 , LYS C:86 , SO4 C:202BINDING SITE FOR RESIDUE SO4 C 203
14BC5SOFTWAREARG C:55 , ASN D:46 , LYS D:49BINDING SITE FOR RESIDUE SO4 C 204
15BC6SOFTWARELYS A:95 , LYS C:39 , VAL D:3 , MET D:4 , LYS D:30 , LYS D:34BINDING SITE FOR RESIDUE SO4 D 201
16BC7SOFTWARETHR D:45 , ASN D:46 , ASN D:47 , LYS D:50 , LYS D:86 , SO4 D:203BINDING SITE FOR RESIDUE SO4 D 202
17BC8SOFTWARELYS D:50 , LYS D:86 , ARG D:102 , GLY D:103 , SO4 D:202 , HOH D:302BINDING SITE FOR RESIDUE SO4 D 203
18BC9SOFTWAREILE D:134 , HIS D:135 , LYS D:136BINDING SITE FOR RESIDUE SO4 D 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WB1)

(-) Exons   (0, 0)

(no "Exon" information available for 3WB1)

(-) 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: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..eeeee..hhhhhhhhhhhhh.....eeee....hhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeee.....eeeeeee........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb1 A   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


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..eeeee..hhhhhhhhhhhhh.....eeee....hhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb1 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....hhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb1 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: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....hhhhhhh.hhhhhhhhhhhhhh...eeeeeee.......eeeeeee....eeeeeee........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wb1 D   2 VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGISI 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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 3WB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WB1)

(-) Gene Ontology  (0, 0)

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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 3wb2 5d5q

(-) Related Entries Specified in the PDB File

3brc HCGB FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS
3wb0
3wb2