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(-) Description

Title :  CRYSTAL STRUCTURE OF COBALAMIN BIOSYNTHESIS PRECORRIN 8W DECARBOXYLASE (CBIT)
 
Authors :  B. Padmanabhan, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Alpha And Beta Protein (A/B) Class, Methyltransferase Superfamily, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Padmanabhan, Y. Bessho, S. Yokoyama
Crystal Structure Of Cobalamin Biosynthesis Precorrin 8W Decarboxylase (Cbit)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE COBALT-PRECORRIN-6Y C(15)-METHYLTRANSFERASE [DECARBOXYLATING]
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBIT
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM 2661
    Synonym: COBALAMIN BIOSYNTHESIS PRECORRIN 8W DECARBOXYLASES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:17 , ILE A:18 , THR A:19 , SER A:46 , GLY A:47 , GLY A:48 , MSE A:49 , HOH A:1056BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREILE B:18 , THR B:19 , SER B:46 , GLY B:47 , GLY B:48 , MSE B:49BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWAREASN A:155 , PHE A:170 , THR B:131 , LEU B:134 , ASN B:155 , PRO B:175 , THR B:177BINDING SITE FOR RESIDUE MES B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YXD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YXD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YXD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YXD)

(-) Exons   (0, 0)

(no "Exon" information available for 2YXD)

(-) 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:180
 aligned with CBIT_METJA | Q57836 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
           CBIT_METJA     4 MIPDEEFIRREGVPITKEEIRAVSIGKLNLNKDDVVVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKINHIVANTIVLENAAKIINEFESRGYNVDAVNVFISYAKKIPSGHMFLAKNPITIIKAVR 183
               SCOP domains d2yxda_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yxd A   4 mIPDEEFIRREGVPITKEEIRAVSIGKLNLNKDDVVVDVGCGSGGmTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKINHIVANTIVLENAAKIINEFESRGYNVDAVNVFISYAKKIPSGHmFLAKNPITIIKAVR 183
                            |       13        23        33        43     |  53        63        73        83        93       103       113       123       133       143       153       163     | 173       183
                            |                                           49-MSE                                                                                                                 169-MSE          
                            4-MSE                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with CBIT_METJA | Q57836 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
           CBIT_METJA     4 MIPDEEFIRREGVPITKEEIRAVSIGKLNLNKDDVVVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKINHIVANTIVLENAAKIINEFESRGYNVDAVNVFISYAKKIPSGHMFLAKNPITIIKAVR 183
               SCOP domains d2yxdb_ B: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yxd B   4 mIPDEEFIRREGVPITKEEIRAVSIGKLNLNKDDVVVDVGCGSGGmTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKINHIVANTIVLENAAKIINEFESRGYNVDAVNVFISYAKKIPSGHmFLAKNPITIIKAVR 183
                            |       13        23        33        43     |  53        63        73        83        93       103       113       123       133       143       153       163     | 173       183
                            4-MSE                                       49-MSE                                                                                                                 169-MSE
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YXD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YXD)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBIT_METJA | Q57836)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    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:0046140    corrin biosynthetic process    The chemical reactions and pathways resulting in the formation of corrin, C19H22N4, the fundamental heterocyclic skeleton of the corrinoids. It consists of four reduced pyrrole rings joined into a macrocyclic ring. Corrin is the core of the vitamin B12 molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

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