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(-) Description

Title :  CRYSTAL STRUCTURE OF PROJECT ID TT0268 FROM THERMUS THERMOPHILUS HB8
 
Authors :  K. Shimizu, N. Kunishima, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  08 Apr 05  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shimizu, N. Kunishima
Crystal Structure Of Project Id Tt0268 From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1X1O)

(-) Sites  (0, 0)

(no "Site" information available for 1X1O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X1O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:285 -Pro A:286
2Arg C:285 -Pro C:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X1O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X1O)

(-) Exons   (0, 0)

(no "Exon" information available for 1X1O)

(-) 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:277
 aligned with Q5SJM3_THET8 | Q5SJM3 from UniProtKB/TrEMBL  Length:286

    Alignment length:277
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
         Q5SJM3_THET8    10 WQGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
               SCOP domains d1x1oa1 A:10-116 automated matches                                                                         d1x1oa2 A:117-286 automated matches                                                                                                                                        SCOP domains
               CATH domains 1x1oA01 A:10-130,A:274-286  [code=3.90.1170.20, no name defined]                                                         1x1oA02 A:131-273 Aldolase class I                                                                                                             1x1oA01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh....eeee...hhhhhhhhhhhh..eee.hhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1o A  10 WQGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with Q5SJM3_THET8 | Q5SJM3 from UniProtKB/TrEMBL  Length:286

    Alignment length:276
                                    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      
         Q5SJM3_THET8    11 QGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
               SCOP domains d1x1ob1 B:11-116 automated matches                                                                        d1x1ob2 B:117-286 automated matches                                                                                                                                        SCOP domains
               CATH domains 1x1oB01 B:11-130,B:274-286  [code=3.90.1170.20, no name defined]                                                        1x1oB02 B:131-273 Aldolase class I                                                                                                             1x1oB01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh....eeee...hhhhhhhhhhhh..eee.hhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1x1o B  11 QGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
                                    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      


Chain C from PDB  Type:PROTEIN  Length:277
 aligned with Q5SJM3_THET8 | Q5SJM3 from UniProtKB/TrEMBL  Length:286

    Alignment length:277
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
         Q5SJM3_THET8    10 WQGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
               SCOP domains d1x1oc1 C:10-116 automated matches                                                                         d1x1oc2 C:117-286 automated matches                                                                                                                                        SCOP domains
               CATH domains 1x1oC01 C:10-130,C:274-286  [code=3.90.1170.20, no name defined]                                                         1x1oC02 C:131-273 Aldolase class I                                                                                                             1x1oC01       CATH domains
           Pfam domains (1) ----------------QRPTase_N-1x1oC01 C:26-115                                                                -QRPTase_C-1x1oC04 C:117-282                                                                                                                                           ---- Pfam domains (1)
           Pfam domains (2) ----------------QRPTase_N-1x1oC02 C:26-115                                                                -QRPTase_C-1x1oC05 C:117-282                                                                                                                                           ---- Pfam domains (2)
           Pfam domains (3) ----------------QRPTase_N-1x1oC03 C:26-115                                                                -QRPTase_C-1x1oC06 C:117-282                                                                                                                                           ---- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhh....eeeee..hhhhhhhhhhhhh....eeee...hhhhhhhhhhhh..eee.hhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1o C  10 WQGGLEEALRAWLREDLGQGDLTSLLVVPEDLEGEAVILAKEGGVLAGLWVAERVFALADPRTAFTPLVAEGARVAEGTEVARVRGPLRGILAGERLALNLLQRLSGIATLTRAYVEALAGTKAQILDTRKTTPGLRALEKYAVRVGGGRNHRYGLFDGILLKENHVRAAGGVGEAVRRAKARAPHYLKVEVEVRSLEELEEALEAGADLILLDNFPLEALREAVRRVGGRVPLEASGNMTLERAKAAAEAGVDYVSVGALTHSAKALDLSLLVVRP 286
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
   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  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Hybrid (58)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q5SJM3_THET8 | Q5SJM3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004514    nicotinate-nucleotide diphosphorylase (carboxylating) activity    Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
    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).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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