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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPLEX OF SAM AND BVU_3255, A METHYLTRANSFERASE FROM BACTEROIDES VULGATUS ATCC 8482
 
Authors :  V. Kumar, J. Sivaraman
Date :  31 Jul 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Small Molecule Methyltransferase, Bvu_3255, Rossmann Fold, Methyltrasnferase, Sam, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Kumar, J. Sivaraman
Structural Characterization Of Bvu_3255, A Methyltransferas From Human Intestine Antibiotic Resistant Pathogen Bacteroides Vulgatus
J. Struct. Biol. 2011
PubMed-ID: 21872662  |  Reference-DOI: 10.1016/J.JSB.2011.08.007

(-) Compounds

Molecule 1 - PUTATIVE METHYLTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGS21A
    Expression System Strain: (DE3)BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BVU_3255
    Organism Scientific: BACTEROIDES VULGATUS
    Organism Taxid: 435590
    Strain: ATCC 8482

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , GLN A:26 , GLY A:27 , GLY A:54 , CYS A:55 , GLY A:56 , GLN A:60 , ASP A:76 , PHE A:77 , PHE A:78 , PHE A:81 , GLY A:103 , SER A:104 , MET A:105 , GLU A:121 , GLY A:122 , ALA A:123 , ASN A:126 , HOH A:287 , HOH A:308 , HOH A:309BINDING SITE FOR RESIDUE SAM A 300
2AC2SOFTWAREARG B:25 , GLN B:26 , GLY B:27 , GLY B:54 , CYS B:55 , GLY B:56 , GLN B:60 , ASP B:76 , PHE B:77 , PHE B:81 , GLY B:103 , SER B:104 , MET B:105 , GLU B:121 , GLY B:122 , ALA B:123 , ASN B:126 , HOH B:320 , HOH B:379BINDING SITE FOR RESIDUE SAM B 300
3AC3SOFTWAREARG C:25 , GLN C:26 , GLY C:27 , GLY C:54 , CYS C:55 , GLY C:56 , GLN C:60 , ASP C:76 , PHE C:77 , PHE C:81 , GLY C:103 , SER C:104 , MET C:105 , GLU C:121 , GLY C:122 , ALA C:123 , ASN C:126 , HOH C:276 , HOH C:280 , HOH C:305BINDING SITE FOR RESIDUE SAM C 300
4AC4SOFTWAREARG D:25 , GLN D:26 , GLY D:27 , GLY D:54 , CYS D:55 , GLY D:56 , GLN D:60 , ASP D:76 , PHE D:77 , PHE D:81 , GLY D:103 , SER D:104 , MET D:105 , GLU D:121 , GLY D:122 , ALA D:123 , ASN D:126 , HOH D:279 , HOH D:337BINDING SITE FOR RESIDUE SAM D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T7S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T7S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T7S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T7S)

(-) Exons   (0, 0)

(no "Exon" information available for 3T7S)

(-) 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:246
 aligned with A6L5C0_BACV8 | A6L5C0 from UniProtKB/TrEMBL  Length:262

    Alignment length:246
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
         A6L5C0_BACV8    14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGFS 259
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh........hhhhhhhhhh.........eeeee....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee............eeeeeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeeee.....hhhhhhhhhhhh...eehhhhhhhhhhh.eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t7s A  14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGFS 259
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      


Chain B from PDB  Type:PROTEIN  Length:239
 aligned with A6L5C0_BACV8 | A6L5C0 from UniProtKB/TrEMBL  Length:262

    Alignment length:245
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253     
         A6L5C0_BACV8    14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGF 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh........hhhhhhhhhh.........eeeee....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee............eeeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeeee.....hhhhhhhhhh.....eehhhhhhhhhhh.eeeeeeee.hhhhh......hhhhhhhhhhhhh------..hhhhhhhhhhhhhhhh..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7s B  14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKH------EELITSNHHEAELYSKYKAYYGYAFFICKKGF 258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      |  -   |   233       243       253     
                                                                                                                                                                                                                                        220    227                               


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with A6L5C0_BACV8 | A6L5C0 from UniProtKB/TrEMBL  Length:262

    Alignment length:245
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253     
         A6L5C0_BACV8    14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGF 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh........hhhhhhhhhh.........eeeee....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhh......eeeee............eeeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeeee.....hhhhhhhhhhhh...eehhhhhhhhhhh.eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7s C  14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGF 258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253     


Chain D from PDB  Type:PROTEIN  Length:235
 aligned with A6L5C0_BACV8 | A6L5C0 from UniProtKB/TrEMBL  Length:262

    Alignment length:248
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253        
         A6L5C0_BACV8    14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQRPAEIHDFWMSAYTEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGFSLR 261
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh........hhhhhhhhhh.........eeeee....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee............eeeeee..hhhhhhhhhhhhhhhh.eeeeeeeeeeeeee....-------------...eehhhhhhhhhhh.eeeeeeee.hhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7s D  14 NLICDFFLNTERQGPGSPEVTLKALSFIDNLTNKSLIADLGCGTGGQTMILAQHVPGKITGIDFFPGFIERFNKNAEKLNLQNRVKGIVGSMDDLSFEKDSLDLIWSEGAIYNIGFERGLKEWRNYLKPGGYLAVSESVWFTDQ-------------TEIDTVPNKVAQIQKAGYIPVATFILPENCWIEHYFAPQAKAEEIFRRKHAGSRIVEELITSNHHEAELYSKYKAYYGYAFFICKKGFSLR 261
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153   |     -       173       183       193       203       213       223       233       243       253        
                                                                                                                                                                         157           171
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  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 3T7S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T7S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T7S)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A6L5C0_BACV8 | A6L5C0)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        A6L5C0_BACV8 | A6L5C0: 3e7p 3t7r 3t7t

(-) Related Entries Specified in the PDB File

3t7r 3t7t