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(-) Description

Title :  THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF
 
Authors :  H. L. Schubert, E. Raux, S. C. Woodcock, K. S. Wilson, M. J. Warren
Date :  01 May 98  (Deposition) - 11 May 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Precorrin-4 Methyltransferase, Methylase, Cobalamin Biosynthesis, Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Schubert, K. S. Wilson, E. Raux, S. C. Woodcock, M. J. Warren
The X-Ray Structure Of A Cobalamin Biosynthetic Enzyme, Cobalt-Precorrin-4 Methyltransferase.
Nat. Struct. Biol. V. 5 585 1998
PubMed-ID: 9665173  |  Reference-DOI: 10.1038/846
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COBALT-PRECORRIN-4 TRANSMETHYLASE
    Atcc: DSM 509
    Cell Line: BL21
    Chains: A
    Collection: DSM 509
    EC Number: 2.1.1.133
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21 (DE3) LYSS
    Expression System Taxid: 562
    Gene: CBIF
    Mutation: YES
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: PRECORRIN-4 METHYLASE, CBIF

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:16 , ARG A:17 , GLY A:18 , SER A:19 , HIS A:20 , GLY A:160 , ARG A:161 , THR A:162 , HOH A:574 , HOH A:576 , HOH A:577BINDING SITE FOR RESIDUE PO4 A 400
2AC2SOFTWAREHIS A:100 , THR A:101 , GLY A:108 , HOH A:504 , HOH A:613BINDING SITE FOR RESIDUE PO4 A 401
3AC3SOFTWAREPRO A:30 , THR A:101 , GLY A:102 , ASP A:103 , MET A:106 , THR A:131 , SER A:132 , PHE A:183 , LEU A:184 , VAL A:210 , LYS A:212 , ALA A:213 , GLN A:240 , ALA A:241 , MET A:242 , HOH A:504 , HOH A:509 , HOH A:519BINDING SITE FOR RESIDUE SAH A 300
4P-4UNKNOWNPO4 A:401 , ALA A:53 , SER A:55 , LEU A:79 , ARG A:98 , GLU A:112 , GLN A:113PRECORRIN-4 BINDING SITE IN DEEP TROUGH. ALSO, LOCATION OF BOUND PHOSPHATE RESIDUE 401. PHOSPHATE PRESENT FROM CRYSTALLIZATION CONDITIONS.
5PALUNKNOWNPO4 A:400PHOSPHATE ION INVOLVED IN CRYSTAL CONTACT.
6SAHUNKNOWNSAH A:300S-ADENOSYL-HOMOCYSTEINE BINDING SITE. CRYSTALS FORMED IN THE PRESENCE OF ADOMET OR ADOHCY.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CBF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CBF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CBF)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUMT_1PS00839 Uroporphyrin-III C-methyltransferase signature 1.CBIF_BACME6-20  1A:26-40
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUMT_1PS00839 Uroporphyrin-III C-methyltransferase signature 1.CBIF_BACME6-20  2A:26-40

(-) Exons   (0, 0)

(no "Exon" information available for 1CBF)

(-) 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:239
 aligned with CBIF_BACME | O87696 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:239
                                    1                                                                                                                                                                                                                                      
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
           CBIF_BACME     - --------MKLYIIGAGPGDPDLITVKGLKLLQQADVVLYADSLVSQDLIAKSKPGAEVLKTAGMHLEEMVGTMLDRMREGKMVVRVHTGDPAMYGAIMEQMVLLKREGVDIEIVPGVTSVFAAAAAAEAELTIPDLTQTVILTRAEGRTPVPEFEKLTDLAKHKCTIALFLSATLTKKVMKEFINAGWSEDTPVVVVYKATWPDEKIVRTTVKDLDDAMRTNGIRKQAMILAGWALDP 231
               SCOP domains d1cbfa_ A: Cobalt precorrin-4 methyltransferase CbiF                                                                                                                                                                                            SCOP domains
               CATH domains 1cbfA01 A:13-130 Cobalt-precorrin-4 Transmethylase; Domain 1                                                          1cbfA02 A:131-251 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.....hhh..hhhhhhhhh..eeee......hhhhhh.....eeee.....hhhhhhhhhhhhhh...eeeee..........hhhhhhhhhh..eeeee....hhhhhhhh.............eeeee........hhh.hhhhhhh..eeeee.....hhhhhhhhhh.......eeeeee.......eeeeeehhhhhhhhhh......eeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------SUMT_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cbf A  13 GLVPRGSHMKLYIIGAGPGDPDLITVKGLKLLQQADVVLYADSLVSQDLIAKSKPGAEVLKTAGMHLEEMVGTMLDRMREGKMVVRVHTGDPAMYGAIMEQMVLLKREGVDIEIVPGVTSVFAAAAAAEAELTIPDLTQTVILTRAEGRTPVPEFEKLTDLAKHKCTIALFLSSTLTKKVMKEFINAGWSEDTPVVVVYKATWPDEKIVRTTVKDLDDAMRTNGIRKQAMILAGWALDP 251
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CBF)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CBIF_BACME | O87696)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0046026    precorrin-4 C11-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-4 = S-adenosyl-L-homocysteine + precorrin 5.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009236    cobalamin biosynthetic process    The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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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 Related Entries

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        CBIF_BACME | O87696: 2cbf

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