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(-) Description

Title :  THE CRYSTAL STRUCTURE AT 1.7 A RESOLUTION OF COBE, A PROTEIN FROM THE COBALAMIN (VITAMIN B12) BIOSYNTHETIC PATHWAY
 
Authors :  J. Vevodova, D. Smith, H. Mcgoldrick, E. Deery, A. G. Murzin, M. J. Warren, K. S. Wilson
Date :  18 Dec 08  (Deposition) - 30 Dec 08  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Biosynthetic Protein, Cobalamin, Cobe, Complete Proteome, Pseudomonas Aeruginosa, Vitamin B12 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vevodova, D. Smith, H. Mcgoldrick, E. Deery, A. G. Murzin, M. J. Warren, K. S. Wilson
The Crystal Structure At 1. 7 A Resolution Of Cobe, A Protein From The Cobalamin (Vitamin B12) Biosynthetic Pathway
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COBE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET14B
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE1Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , ALA A:90 , SER A:98 , VAL A:99 , ALA A:100 , LYS A:122 , SER A:129 , HOH A:2095BINDING SITE FOR RESIDUE SO4 A1140
2AC2SOFTWARECYS A:19 , SER A:20 , HIS A:23 , SER A:87 , ALA A:88 , VAL A:89 , HOH A:2078BINDING SITE FOR RESIDUE SO4 A1141
3AC3SOFTWARECYS A:15 , ARG A:17 , GLY A:18 , CYS A:19 , ARG A:52 , ASP A:53 , GLU A:54 , PRO A:55 , GLY A:56 , LEU A:57 , ASP A:126 , HOH A:2096BINDING SITE FOR RESIDUE GOL A1142
4AC4SOFTWAREASP A:49 , GLU A:54 , ARG A:58 , PHE A:70 , PRO A:81BINDING SITE FOR RESIDUE GOL A1143
5AC5SOFTWAREARG A:16 , ARG A:17 , ARG A:127 , HOH A:2084 , HOH A:2097BINDING SITE FOR RESIDUE GOL A1144

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W6K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W6K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W6K)

(-) Exons   (0, 0)

(no "Exon" information available for 2W6K)

(-) 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:142
 aligned with Q9HZQ0_PSEAE | Q9HZQ0 from UniProtKB/TrEMBL  Length:142

    Alignment length:142
                               1                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137  
         Q9HZQ0_PSEAE     - ---MPLPIPSLLIAGIGCRRGCSAEHLRALLERTLGEHGRSLAELDALASIDGKRDEPGLRQLATLLERPVHFLAPAVLHDYEPRLLSPSAVALRETGCSSVAEAAALALAERLGGGRADLLGAKRSDDRASIALARLLTER 139
               SCOP domains ---d2w6ka1 A:1-139 Cobalamin biosynthesis protein CobE                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------CbiG_C-2w6kA01 A:8-134                                                                                                         ----- Pfam domains
         Sec.struct. author ...........eeeeeee....hhhhhhhhhhhhhhhh..hhhhh.eeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh..eee....ee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w6k A  -2 GSHmPLPIPSLLIAGIGCRRGCSAEHLRALLERTLGEHGRSLAELDALASIDGKRDEPGLRQLATLLERPVHFLAPAVLHDYEPRLLSPSAVALRETGCSSVAEAAALALAERLGGGRADLLGAKRSDDRASIALARLLTER 139
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137  
                               |                                                                                                                                          
                               1-MSE
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W6K)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CbiG_C] (2)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9HZQ0_PSEAE | Q9HZQ0)
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.

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 Related Entries

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        Q9HZQ0_PSEAE | Q9HZQ0: 2w6l

(-) Related Entries Specified in the PDB File

2w6l THE CRYSTAL STRUCTURE AT 1.7 A RESOLUTION OF COBE, A PROTEIN FROM THE COBALAMIN ( VITAMIN B12) BIOSYNTHETIC PATHWAY