Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  2.00 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A QUINOLINATE PHOSPHORIBOSYLTRANSFERASE FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
 
Authors :  A. S. Halavaty, G. Minasov, J. Winsor, I. Dubrovska, L. Shuvalova, S. Pe W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  19 Oct 10  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Nicotinate-Nucleotide Pyrophosphorylase, Pyridine- 2, 3- Dicarboxylate, 5-Phospho-Alpha-D-Ribose 1-Diphosphate, Center For Structural Genomics Of Infectious Diseases, Csgid, Guinolinate Phosphoribosyltransferase, De Novo Synthesis Of Nad, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, G. Minasov, J. Winsor, I. Dubrovska, L. Shuvalova, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 00 Angstrom Resolution Crystal Structure Of A Quinolinate Phosphoribosyltransferase From Vibrio Cholerae O1 Biovar Eltor Str. N16961
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE, CARBOXYLATING
    Chains: A, B
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)/MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VC_2422
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961

 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
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:302 , HOH B:374 , HOH B:381 , HOH B:401 , HOH B:437 , HOH B:438BINDING SITE FOR RESIDUE MG B 297

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PAJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PAJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PAJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PAJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3PAJ)

(-) 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:302
 aligned with Q9KPE6_VIBCH | Q9KPE6 from UniProtKB/TrEMBL  Length:296

    Alignment length:302
                                  1                                                                                                                                                                                                                                                                                                       
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
         Q9KPE6_VIBCH     - ------MKETHNSQDRLAYLKQQLPADITRSVIDTLKEDLGGTLDPAADITASLIPADRISTATIITREAGVFCGQLWADEVFKQLGGQVSIEWHVQDGDTLTPNQTLCTLTGPARILLTGERNAMNFIQTLSGCATATARYVQELKGTQCRLLDTRKTIPGLRSALKYAVACGGGYNHRIGVFDAYLIKENHIIACGGIRQAISTAKQLNPGKPVEVETETLAELEEAISAGADIIMLDNFSLEMMREAVKINAGRAALENSGNITLDNLKECAETGVDYISVGALTKHLKALDLSMRFKS 296
               SCOP domains d3paja1 A:-5-128 automated matches                                                                                                    d3paja2 A:129-296 automated matches                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhh....eeeeeeee...ee..hhhhhhhhhhhh....eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eee.hhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3paj A  -5 YFQSNAMKETHNSQDRLAYLKQQLPADITRSVIDTLKEDLGGTLDPAADITASLIPADRISTATIITREAGVFCGQLWADEVFKQLGGQVSIEWHVQDGDTLTPNQTLCTLTGPARILLTGERNAMNFIQTLSGCATATARYVQELKGTQCRLLDTRKTIPGLRSALKYAVACGGGYNHRIGVFDAYLIKENHIIACGGIRQAISTAKQLNPGKPVEVETETLAELEEAISAGADIIMLDNFSLEMMREAVKINAGRAALENSGNITLDNLKECAETGVDYISVGALTKHLKALDLSMRFKS 296
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q9KPE6_VIBCH | Q9KPE6 from UniProtKB/TrEMBL  Length:296

    Alignment length:297
                               1                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
         Q9KPE6_VIBCH     - ---MKETHNSQDRLAYLKQQLPADITRSVIDTLKEDLGGTLDPAADITASLIPADRISTATIITREAGVFCGQLWADEVFKQLGGQVSIEWHVQDGDTLTPNQTLCTLTGPARILLTGERNAMNFIQTLSGCATATARYVQELKGTQCRLLDTRKTIPGLRSALKYAVACGGGYNHRIGVFDAYLIKENHIIACGGIRQAISTAKQLNPGKPVEVETETLAELEEAISAGADIIMLDNFSLEMMREAVKINAGRAALENSGNITLDNLKECAETGVDYISVGALTKHLKALDLSMRF 294
               SCOP domains d3pajb1 B:-2-128 automated matches                                                                                                 d3pajb2 B:129-294 automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------QRPTase_N-3pajB01 B:40-127                                                              -QRPTase_C-3pajB03 B:129-293                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) ------------------------------------------QRPTase_N-3pajB02 B:40-127                                                              -QRPTase_C-3pajB04 B:129-293                                                                                                                                          - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhh....eeeeeeee...ee..hhhhhhhhhhhh....eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhhh....eee.hhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3paj B  -2 SNAMKETHNSQDRLAYLKQQLPADITRSVIDTLKEDLGGTLDPAADITASLIPADRISTATIITREAGVFCGQLWADEVFKQLGGQVSIEWHVQDGDTLTPNQTLCTLTGPARILLTGERNAMNFIQTLSGCATATARYVQELKGTQCRLLDTRKTIPGLRSALKYAVACGGGYNHRIGVFDAYLIKENHIIACGGIRQAISTAKQLNPGKPVEVETETLAELEEAISAGADIIMLDNFSLEMMREAVKINAGRAALENSGNITLDNLKECAETGVDYISVGALTKHLKALDLSMRF 294
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PAJ)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KPE6_VIBCH | Q9KPE6)
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:0006734    NADH metabolic process    The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006739    NADP metabolic process    The chemical reactions and pathways involving nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; metabolism may be of either the oxidized form, NADP, or the reduced form, NADPH.
    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.
    GO:0034213    quinolinate catabolic process    The chemical reactions and pathways resulting in the breakdown of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3paj)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3paj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9KPE6_VIBCH | Q9KPE6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.19
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9KPE6_VIBCH | Q9KPE6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3PAJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PAJ)