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(-) Description

Title :  MT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M. THERMOAUTOTROPHICUM, C2 SPACEGROUP WITH SHORT CELL
 
Authors :  J. P. Keller, P. M. Smith, J. Benach, D. Christendat, G. Detitta, J. F. Hunt
Date :  26 Feb 02  (Deposition) - 27 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Beta Barrel, Rossmann Fold, Tetramer, Methyltransferase, Decarboxylase, Structure-Based Function Assignment, Transferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Keller, P. M. Smith, J. Benach, D. Christendat, G. Detitta, J. F. Hunt
The Crystal Structure Of Mt0146/Cbit Suggests That The Putative Precorrin-8W Decarboxylase Is A Methyltransferase
Structure V. 10 1475 2002
PubMed-ID: 12429089  |  Reference-DOI: 10.1016/S0969-2126(02)00876-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRECORRIN-6Y METHYLTRANSFERASE/PUTATIVE DECARBOXYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: B834 CODON+
    Expression System Taxid: 562
    Gene: MTH146
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262
    Synonym: MT0146, CBIT, MTH146

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric/Biological Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1L3C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L3C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:15 -Pro A:16
2Gly B:15 -Pro B:16
3Gly C:15 -Pro C:16
4Gly D:15 -Pro D:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L3C)

(-) Exons   (0, 0)

(no "Exon" information available for 1L3C)

(-) 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:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
           CBIT_METTH     1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV 186
               SCOP domains d1l3ca_ A: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1l3cA00 A:2-186 Vaccinia Virus protein VP39                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3c A   1 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 186
                            |       10        20     |  30        40        50        60        70  |     80      | 90       100       110       120       130       140   |   150       160       170 ||    180      
                            |                19-MSE 26-MSE                                         73-MSE        87-MSE                                                  144-MSE                     172-MSE          
                            1-MSE                                                                                                                                                                     173-MSE         


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
           CBIT_METTH     1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV 186
               SCOP domains d1l3cb_ B: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1l3cB00 B:2-186 Vaccinia Virus protein VP39                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3c B   1 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 186
                            |       10        20     |  30        40        50        60        70  |     80      | 90       100       110       120       130       140   |   150       160       170 ||    180      
                            1-MSE            19-MSE 26-MSE                                         73-MSE        87-MSE                                                  144-MSE                     172-MSE          
                                                                                                                                                                                                      173-MSE         


Chain C from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
           CBIT_METTH     1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV 186
               SCOP domains d1l3cc_ C: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1l3cC00 C:2-186 Vaccinia Virus protein VP39                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3c C   1 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 186
                            |       10        20     |  30        40        50        60        70  |     80      | 90       100       110       120       130       140   |   150       160       170 ||    180      
                            1-MSE            19-MSE 26-MSE                                         73-MSE        87-MSE                                                  144-MSE                     172-MSE          
                                                                                                                                                                                                      173-MSE         


Chain D from PDB  Type:PROTEIN  Length:186
 aligned with CBIT_METTH | O26249 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
           CBIT_METTH     1 MIPDDEFIKNPSVPGPTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFDVNITELNIARGRALDRGTMMVSRNPVALIYTGV 186
               SCOP domains d1l3cd_ D: Precorrin-6Y methyltransferase (CbiT)                                                                                                                                           SCOP domains
               CATH domains -1l3cD00 D:2-186 Vaccinia Virus protein VP39                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh...eeeeee.....hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeeeee....eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3c D   1 mIPDDEFIKNPSVPGPTAmEVRCLImCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEmNLQRHGLGDNVTLmEGDAPEALCKIPDIDIAVVGGSGGELQEILRIIKDKLKPGGRIIVTAILLETKFEAmECLRDLGFDVNITELNIARGRALDRGTmmVSRNPVALIYTGV 186
                            |       10        20     |  30        40        50        60        70  |     80      | 90       100       110       120       130       140   |   150       160       170 ||    180      
                            1-MSE            19-MSE 26-MSE                                         73-MSE        87-MSE                                                  144-MSE                     172-MSE          
                                                                                                                                                                                                      173-MSE
   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  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L3C)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CBIT_METTH | O26249)
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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  1l3c
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBIT_METTH | O26249: 1f38 1kxz 1l3b 1l3i

(-) Related Entries Specified in the PDB File

1f38 P 21 21 2 SPACE GROUP
1kxz P 1 SPACE GROUP
1l3b C 2 SPACE GROUP, LONG CELL
1l3i ADOHCY BINARY COMPLEX