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(-) Description

Title :  CRYSTAL STRUCTURE OF COBALAMIN BIOSYNTHESIS PRECORRIN-6Y METHYLASE (CBIE) FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  Y. Kim, A. Joachimiak, X. Xu, A. Savchenko, A. Edwards, Midwest Center Structural Genomics (Mcsg)
Date :  17 Oct 05  (Deposition) - 29 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Beta, Alpha-Beta-Alpha Sandwich, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, X. Xu, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Cobalamin Biosynthesis Precorrin-6Y Methylase (Cbie) From Archaeoglobus Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COBALAMIN BIOSYNTHESIS PRECORRIN-6Y METHYLASE (CBIE)
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CBIE
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:74 , GLY A:75 , ASP A:76 , VAL A:79 , ALA A:80 , SER A:102 , SER A:103 , LEU A:144 , ALA A:145 , LEU A:165 , MSE A:167 , ASP A:185 , TYR A:186 , THR A:187 , ILE A:188 , HOH A:208 , HOH A:213 , HOH A:225 , HOH A:292BINDING SITE FOR RESIDUE SAH A 201
2AC2SOFTWARETHR B:74 , GLY B:75 , ASP B:76 , VAL B:79 , ALA B:80 , SER B:102 , SER B:103 , LEU B:144 , ALA B:145 , LEU B:162 , LEU B:165 , MSE B:167 , ASP B:185 , TYR B:186 , THR B:187 , ILE B:188 , HOH B:376BINDING SITE FOR RESIDUE SAH B 203

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:10 -A:166
2B:10 -B:166

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BB3)

(-) Exons   (0, 0)

(no "Exon" information available for 2BB3)

(-) 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:194
 aligned with O29536_ARCFU | O29536 from UniProtKB/TrEMBL  Length:197

    Alignment length:198
                               1                                                                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187        
         O29536_ARCFU     - ---MIWIVGSGTCRGQTTERAKEIIERAEVIYGSRRALELAGVVDDSRARILRSFKGDEIRRIMEEGREREVAVISTGDPMVAGLGRVLREIAEDVEIKIEPAISSVQVALARLKVDLSEVAVVDCHAKDFDAELTELLKYRHLLILADSHFPLERLGKRRVVLLENLCMEGERIREGNADSIELESDYTIIFVEREV 195
               SCOP domains ---d2bb3a1 A:1-195 Precorrin-6y methylase CbiE                                                                                                                                                         SCOP domains
               CATH domains 2bb3A01 A:-2-102 Cobalt-precorrin-4 Transmethylase; Domain 1                                             2bb3A02 A:103-195 Met    hyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhh.eeeehhhhhhhh.......eee....hhhhhhhhhhhhhhh.eeeee........hhhhhhh.....eeeee...hhhhhhhhhhh.hhh.eeeee.----.hhhhhhhhhhheeeeee.....hhhhh..eeeeee.......eeeeee..........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bb3 A  -2 SGHmIWIVGSGTCRGQTTERAKEIIERAEVIYGSRRALELAGVVDDSRARILRSFKGDEIRRImEEGREREVAVISTGDPmVAGLGRVLREIAEDVEIKIEPAISSVQVALARLKVDLSEVAVVDC----FDAELTELLKYRHLLILADSHFPLERLGKRRVVLLENLCmEGERIREGNADSIELESDYTIIFVEREV 195
                               |     7        17        27        37        47        57   |    67        77|       87        97       107       117     |   -|      137       147       157       167       177       187        
                               |                                                          61-MSE           78-MSE                                      123  128                                    167-MSE                        
                               1-MSE                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with O29536_ARCFU | O29536 from UniProtKB/TrEMBL  Length:197

    Alignment length:197
                              1                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       
         O29536_ARCFU     - --MIWIVGSGTCRGQTTERAKEIIERAEVIYGSRRALELAGVVDDSRARILRSFKGDEIRRIMEEGREREVAVISTGDPMVAGLGRVLREIAEDVEIKIEPAISSVQVALARLKVDLSEVAVVDCHAKDFDAELTELLKYRHLLILADSHFPLERLGKRRVVLLENLCMEGERIREGNADSIELESDYTIIFVEREV 195
               SCOP domains d2bb3b_ B: Precorrin-6y methylase CbiE                                                                                                                                                                SCOP domains
               CATH domains 2bb3B01 B:-1-102 Cobalt-precorrin-4 Transmethylase; Domain 1                                            2bb3B02 B:103-195 Meth     yltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhhh.eeeehhhhhhhh.......eee....hhhhhhhhhhhhhhh.eeeee........hhhhhh......eeeee...hhhhhhhhhhh.hhh.eeeee..-----....hhhhh.eeeeee....hhhhhh..eeeeee.......eeeeee.hhh......eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bb3 B  -1 GHmIWIVGSGTCRGQTTERAKEIIERAEVIYGSRRALELAGVVDDSRARILRSFKGDEIRRImEEGREREVAVISTGDPmVAGLGRVLREIAEDVEIKIEPAISSVQVALARLKVDLSEVAVVDCH-----AELTELLKYRHLLILADSHFPLERLGKRRVVLLENLCmEGERIREGNADSIELESDYTIIFVEREV 195
                              |      8        18        28        38       |48     |||58  |   ||68        78        88        98       108       118     |   - |     138       148  |||| 158       368|   |||178       188       
                              1-MSE                                       46||    54||    |  65||         78-MSE                                       124   130                  151|||          167-MSE73||                    
                                                                          247|    255|    |  266|                                                                                  352||           368|  374|                    
                                                                            48      56    |    67                                                                                   353|            169   175                    
                                                                                         61-MSE                                                                                      154
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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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BB3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O29536_ARCFU | O29536)
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.
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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