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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF PRECORRIN-6Y C5,15-METHYLTRANSFERASE FROM RHODOBACTER CAPSULATUS
 
Authors :  A. Seyedarabi, R. W. Pickersgill
Date :  17 Jun 10  (Deposition) - 08 Jun 11  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Methyltransferase, Decarboxylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Deery, S. Schroeder, A. D. Lawrence, S. L. Taylor, A. Seyedarabi, J. Waterman, K. S. Wilson, D. Brown, M. A. Geeves, M. J. Howard, R. W. Pickersgill, M. J. Warren
An Enzyme-Trap Approach Allows Isolation Of Intermediates I Cobalamin Biosynthesis.
Nat. Chem. Biol. V. 8 933 2012
PubMed-ID: 23042036  |  Reference-DOI: 10.1038/NCHEMBIO.1086

(-) Compounds

Molecule 1 - PRECORRIN-6Y METHYLASE
    Chains: A, B
    EC Number: 2.1.1.132
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 214-396
    Gene: COBL
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 272942
    Strain: SB1003

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PG42Ligand/IonTETRAETHYLENE GLYCOL
3SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:16 , ILE A:17 , THR A:18 , GLY A:42 , GLY A:43 , GLY A:44 , SER A:45 , GLY A:46 , SER A:47 , ILE A:62 , GLU A:63 , PRO A:64 , ARG A:68 , THR A:91 , ALA A:92 , GLY A:110BINDING SITE FOR RESIDUE SAH A 300
2AC2SOFTWAREGLU A:139 , TRP A:170 , PRO A:175 , GLU B:139 , TRP B:170BINDING SITE FOR RESIDUE GOL A 1448
3AC3SOFTWAREGLN B:16 , ILE B:17 , THR B:18 , GLY B:42 , GLY B:43 , GLY B:44 , SER B:45 , SER B:47 , GLU B:63 , PRO B:64 , ARG B:68 , ALA B:92BINDING SITE FOR RESIDUE SAH B 300
4AC4SOFTWAREALA A:12 , HIS A:13 , LYS A:74 , SER B:9 , ALA B:10 , HIS B:13 , THR B:78 , TYR B:79BINDING SITE FOR RESIDUE PG4 B 321
5AC5SOFTWAREPRO B:21 , GLN B:160 , SER B:171BINDING SITE FOR RESIDUE GOL B 1449

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:92 -Pro A:93
2Ser B:82 -Pro B:83
3Ala B:92 -Pro B:93
4Leu B:164 -Gly B:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NJR)

(-) 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:184
 aligned with D5AV04_RHOCB | D5AV04 from UniProtKB/TrEMBL  Length:396

    Alignment length:184
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
         D5AV04_RHOCB   213 LSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 396
               SCOP domains d3njra_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhh......eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeee..eeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njr A   0 MSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain A from PDB  Type:PROTEIN  Length:184
 aligned with O68099_RHOCA | O68099 from UniProtKB/TrEMBL  Length:396

    Alignment length:184
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
         O68099_RHOCA   213 LSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 396
               SCOP domains d3njra_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhh......eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeee..eeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njr A   0 MSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with D5AV04_RHOCB | D5AV04 from UniProtKB/TrEMBL  Length:396

    Alignment length:184
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
         D5AV04_RHOCB   213 LSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 396
               SCOP domains d3njrb_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------Methyltransf_18-3njrB01 B:34-134                                                                     ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Methyltransf_18-3njrB02 B:34-134                                                                     ------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhh......eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeee....eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njr B   0 MSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with O68099_RHOCA | O68099 from UniProtKB/TrEMBL  Length:396

    Alignment length:184
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
         O68099_RHOCA   213 LSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 396
               SCOP domains d3njrb_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------Methyltransf_18-3njrB01 B:34-134                                                                     ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------Methyltransf_18-3njrB02 B:34-134                                                                     ------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhh......eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeeeee....eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njr B   0 MSQVPGRPESAFAHDGQITKSPMRALTLAALAPRRGELLWDIGGGSGSVSVEWCLAGGRAITIEPRADRIENIQKNIDTYGLSPRMRAVQGTAPAALADLPLPEAVFIGGGGSQALYDRLWEWLAPGTRIVANAVTLESETLLTQLHARHGGQLLRIDIAQAEPLGRMRGWSASRPQLQWSGQR 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (D5AV04_RHOCB | D5AV04)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0046025    precorrin-6Y C5,15-methyltransferase (decarboxylating) activity    Catalysis of the reaction: 2 S-adenosyl-L-methionine + precorrin-6Y = 2 S-adenosyl-L-homocysteine + precorrin-8X + CO2.
    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: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: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.

Chain A,B   (O68099_RHOCA | O68099)
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: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: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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  3njr
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 Related Entries

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