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(-) Description

Title :  CRYSTAL STRUCTURE OF PRECORRIN-6A SYNTHASE FROM RHODOBACTER CAPSULATUS
 
Authors :  A. Seyedarabi, R. W. Pickersgill
Date :  06 Jun 10  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Deacetylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Seyedarabi, R. W. Pickersgill
Crystal Structure Of Precorrin-6A Synthase From Rhodobacter Capsulatus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PRECORRIN-6A SYNTHASE/COBF PROTEIN
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCOBF
    Organism CommonRHODOPSEUDOMONAS CAPSULATA
    Organism ScientificRHODOBACTER CAPSULATUS
    Organism Taxid272942
    StrainSB1003

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:11 , TRP A:112 , GLY A:113 , ASP A:114 , LEU A:117 , TYR A:118 , THR A:143 , ALA A:144 , MET A:186 , LEU A:187 , CYS A:208 , VAL A:209 , MET A:243 , ASP A:244 , ILE A:245 , HOH A:319 , HOH A:444 , HOH A:458 , HOH A:462BINDING SITE FOR RESIDUE SAH A 300
2AC2SOFTWAREALA A:151 , GLU A:214 , HOH A:356 , HOH A:409 , HOH A:448 , HOH B:310BINDING SITE FOR RESIDUE ACT A 2382
3AC3SOFTWAREGLN A:146 , LEU A:156 , GLN B:146BINDING SITE FOR RESIDUE ACT A 2384
4AC4SOFTWARETHR B:11 , TRP B:112 , GLY B:113 , ASP B:114 , LEU B:117 , TYR B:118 , THR B:143 , ALA B:144 , MET B:186 , LEU B:187 , CYS B:208 , VAL B:209 , MET B:243 , ASP B:244 , ILE B:245 , HOH B:282 , HOH B:354 , HOH B:444 , HOH B:487 , HOH B:490BINDING SITE FOR RESIDUE SAH B 300
5AC5SOFTWAREHOH A:281 , HOH A:304 , ALA B:151 , GLU B:214 , HOH B:312 , HOH B:337BINDING SITE FOR RESIDUE ACT B 2383

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ND1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ND1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ND1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ND1)

(-) Exons   (0, 0)

(no "Exon" information available for 3ND1)

(-) 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:244
 aligned with D5AV00_RHOCB | D5AV00 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                             1                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
         D5AV00_RHOCB     - -MIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASNPSYRKGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeee.....---------hhhhhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhh......eeeeee...hhhhhhhhhhh.........eeeeehhhhhhhh......eeeee....hhhhhh....eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd1 A   0 HMIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVR---------GVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
                                     9        19        29        39        49        59        69|        -|       89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
                                                                                                 70        80                                                                                                                                                                            

Chain A from PDB  Type:PROTEIN  Length:244
 aligned with O68102_RHOCA | O68102 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                             1                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
         O68102_RHOCA     - -MIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASNPSYRKGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeee.....---------hhhhhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhh......eeeeee...hhhhhhhhhhh.........eeeeehhhhhhhh......eeeee....hhhhhh....eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd1 A   0 HMIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVR---------GVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
                                     9        19        29        39        49        59        69|        -|       89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
                                                                                                 70        80                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with D5AV00_RHOCB | D5AV00 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                             1                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
         D5AV00_RHOCB     - -MIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASNPSYRKGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TP_methylase-3nd1B01 B:3-225                                                                                                                                                                                                   --------------------------- Pfam domains (1)
           Pfam domains (2) ---TP_methylase-3nd1B02 B:3-225                                                                                                                                                                                                   --------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeee.........----hhhhhhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhh....eeeeee...hhhhhhhhhhh.........eeeeehhhhhhhh......eeeee....hhhhhh....eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd1 B   0 HMIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASN----KGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
                                     9        19        29        39        49        59        69    |   79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
                                                                                                     74   79                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with O68102_RHOCA | O68102 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                             1                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
         O68102_RHOCA     - -MIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASNPSYRKGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TP_methylase-3nd1B01 B:3-225                                                                                                                                                                                                   --------------------------- Pfam domains (1)
           Pfam domains (2) ---TP_methylase-3nd1B02 B:3-225                                                                                                                                                                                                   --------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeee.........----hhhhhhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhh....eeeeee...hhhhhhhhhhh.........eeeeehhhhhhhh......eeeee....hhhhhh....eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd1 B   0 HMIELSLIGIGTGNPRHITGQAVDAMNAADLILIPLKGADKSDLAGLRRQICAAHLTNPATKVIDFALPVRDASN----KGVDDWHDAIAETWLSEITAHVPGLEGRVALLVWGDPSLYDSTLRIAERLKSRLPLTTKVIPGITAIQALCAAHAIPLNDIGAPVVITTGRQLRDHGWPAGTETVVAMLDGECSFQSLPPDGLTIFWGACVAMPEEVLIRGPVAEVTDEILQARADLRARHGWVMDIYLLRRNV 252
                                     9        19        29        39        49        59        69    |   79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   
                                                                                                     74   79                                                                                                                                                                             

   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  (0, 0)

(no "SCOP Domain" information available for 3ND1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ND1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D5AV00_RHOCB | D5AV00)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0043819    precorrin-6A synthase (deacetylating) activity    Catalysis of the reaction: S-adenosyl-L-methionine + H(2)O + precorrin-5 = S-adenosyl-L-homocysteine + acetate + 2 H(+) + precorrin-6X.
    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.

Chain A,B   (O68102_RHOCA | O68102)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0043819    precorrin-6A synthase (deacetylating) activity    Catalysis of the reaction: S-adenosyl-L-methionine + H(2)O + precorrin-5 = S-adenosyl-L-homocysteine + acetate + 2 H(+) + precorrin-6X.
    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.

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