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(-) Description

Title :  CRYSTAL STRUCTURE OF NICTINATE-NUCLEOTIDE-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Asada, N. Kunishima, Riken Structural Genomics/Proteomics Ini (Rsgi)
Date :  19 Jan 05  (Deposition) - 01 Feb 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Thermus Thermophilus Hb8, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Asada, N. Kunishima
Crystal Structure Of Nictinate-Nucleotide-Dimethylbenzimidazole Phosphoribosyltransferase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:127 , GLU A:153 , HOH A:1034 , HOH A:1035 , HOH A:1045 , HOH A:1057BINDING SITE FOR RESIDUE NA A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WX1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WX1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WX1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WX1)

(-) Exons   (0, 0)

(no "Exon" information available for 1WX1)

(-) 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:330
 aligned with COBT_THET8 | Q7SIC7 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:335
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330     
           COBT_THET8     1 MDPEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVGRGTGVGEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
               SCOP domains d1wx1a_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wx1A01 A:1-43,A:317-335                   1wx1A02 A:44-316  [code=3.40.50.10210, no name defined]                                                                                                                                                                                                                          1wx1A01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........eeeeeeee.hhhhhhh......hhhhhhhhhhhh..hhhhhhhhhh.eeeeeeeee..........eee................hhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.hhhhhh.-----hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh.eee......hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wx1 A   1 MDPEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVG-----GEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -   |   200       210       220       230       240       250       260       270       280       290       300       310       320       330     
                                                                                                                                                                                                                     188   194                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with COBT_THET8 | Q7SIC7 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:335
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330     
           COBT_THET8     1 MDPEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVGRGTGVGEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
               SCOP domains d1wx1b_ B: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1wx1B01 B:1-43,B:317-335                   1wx1B02 B:44-316  [code=3.40.50.10210, no name defined]                                                                                                                                                                                                                          1wx1B01             CATH domains
           Pfam domains (1) DBI_PRT-1wx1B01 B:1-332                                                                                                                                                                                                                                                                                                                     --- Pfam domains (1)
           Pfam domains (2) DBI_PRT-1wx1B02 B:1-332                                                                                                                                                                                                                                                                                                                     --- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........eeeeeeee.hhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhh.eeeeeeeee..........eee................hhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh..hhhhhh.-----hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh.eee......hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wx1 B   1 MDPEVFAQARLRMDQLTKPPRALGYLEEVALRLAALQGRVKPELGRGAVVVAAADHGVVAEGVSAYPQEVTRQMVLNFLRGGAAINQFALAADCAVYVLDVGVVGELPDHPGLLKRKVRPGTANLAQGPAMTPEEAERALLAGREAARRAIAEGATLLAAGDMGIGNTTAAAALTAALLGLPPEAVVG-----GEEGLRRKRQAVARALARLHPGMGPLEVAAEVGGLELVAIAGIYLEGYEAGLPLVLDGFPVTAGALLAWKMAPGLRDHLFAGHLSREPGHRHQLEALGLRPLLDLDLALGEGTGAVLAMPLLRAAARILHMATFQEAGVSRG 335
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -   |   200       210       220       230       240       250       260       270       280       290       300       310       320       330     
                                                                                                                                                                                                                     188   194
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DBI_PRT] (24)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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