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(-) Description

Title :  CRYSTAL STRUCTURE OF COBT FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. Kunishima, Y. Asada, M. Miyano, Riken Structural Genomics/Prote Initiative (Rsgi)
Date :  17 Jan 03  (Deposition) - 04 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phosphoribosyltransferase, Cobalamin Biosynthesis, Vitamin B12, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kunishima, Y. Asada, M. Miyano
Crystal Structure Of Cobt From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COBT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J33)

(-) Sites  (0, 0)

(no "Site" information available for 1J33)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J33)

(-) Exons   (0, 0)

(no "Exon" information available for 1J33)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:333
 aligned with COBT_THET8 | Q7SIC7 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:333
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   
           COBT_THET8     3 PEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVGRGTGVGEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
               SCOP domains d1j33a_ A: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j33A01 A:3-43,A:317-335                 1j33A02 A:44-316  [code=3.40.50.10210, no name defined]                                                                                                                                                                                                                          1j33A01             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh........hhhhhhhhhhhhhhhh........eeeeeeee.hhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhh.eeeeeeeee..........eee................hhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j33 A   3 PEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVGRGTGVGEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGIELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   

   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 Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J33)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (COBT_THET8 | Q7SIC7)
molecular function
    GO:0015420    cobalamin-transporting ATPase activity    Catalysis of the reaction: ATP + H2O + cob(III)alamin(out) = ADP + phosphate + cob(III)alamin(in). Cobalamin is also known as vitamin B12.
    GO:0008939    nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity    Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0009163    nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0035461    vitamin transmembrane transport    The process in which a vitamin is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.

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 Related Entries

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        COBT_THET8 | Q7SIC71wx1

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