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

(-) Description

Title :  CRYSTAL STRUCTURE OF A NICOTINATE PHOSPHORIBOSYLTRANSFERASE
 
Authors :  J. Seetharaman, S. Swaminathan, S. K. Burley, New York Sgx Research For Structural Genomics (Nysgxrc)
Date :  20 Dec 04  (Deposition) - 11 Jan 05  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Nysgxrc, T1764, Psi, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, S. Swaminathan
Crystal Structure Of A Nicotinate Phosphoribosyltransferase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PNCB
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: NAPRTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YBE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YBE)

(-) 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:416
 aligned with PNCB_AGRFC | Q8UIS9 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:426
                                    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       340       350       360       370       380       390       400       410       420      
           PNCB_AGRFC     1 MTKTDIATRVHNHTWKLDPIVRSLIDTDFYKLLMLQMIWKLYPEVDATFSLINRTKTVRLAEEIDEMELREQLDHARTLRLSKKENIWLAGNTFYGRSQIFEPEFLSWLSSYQLPEYELFKRDGQYELNFHGRWMDTTLWEIPALSIINELRSRSAMRSLGYFTLDVLYARAKAKMWEKVERLRELPGLRISDFGTRRRHSFLWQRWCVEALKEGIGPAFTGTSNVLLAMDSDLEAVGTNAHELPMVVAALAQTNEELAAAPYQVLKDWNRLYGGNLLIVLPDAFGTAAFLRNAPEWVADWTGFRPDSAPPIEGGEKIIEWWRKMGRDPRTKMLIFSDGLDVDAIVDTYRHFEGRVRMSFGWGTNLTNDFAGCAPKTIASLKPISIVCKVSDANGRPAVKLSDNPQKATGDPAEVERYLKFFGEED 426
               SCOP domains d1ybea2 A     :8-167 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                                    d1ybea1 A:168-433 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                                  SCOP domains
               CATH domains 1ybeA00 A     :8-433 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.-----.............hhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhhh......eeee....eeeee..hhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......eee.......hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhh.hhhhhhh.ee.....hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh.......-----.....eeeeeeee..ee......hhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ybe A   8 MTKTDIATR-----WKLDPIVRSLIDTDFYKLLMLQMIWKLYPEVDATFSLINRTKTVRLAEEIDEMELREQLDHARTLRLSKKENIWLAGNTFYGRSQIFEPEFLSWLSSYQLPEYELFKRDGQYELNFHGRWMDTTLWEIPALSIINELRSRSAMRSLGYFTLDVLYARAKAKMWEKVERLRELPGLRISDFGTRRRHSFLWQRWCVEALKEGIGPAFTGTSNVLLAMDSDLEAVGTNAHELPMVVAALAQTNEELAAAPYQVLKDWNRLYGGNLLIVLPDAFGTAAFLRNAPEWVADWTGFRPDSAPPIEGGEKIIEWWRKMGRDPRTKMLIFSDGLDVDAIVDTYRHFEGRVRMSFGWGTNLTNDFAGCAP-----LKPISIVCKVSDANGRPAVKLSDNPQKATGDPAEVERYLKFFGEED 433
                                    |-    |   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       297       307       317       327       337       347       357       367       377    |    -|      397       407       417       427      
                                   16    22                                                                                                                                                                                                                                                                                                                                                                     382   388                                             


Chain B from PDB  Type:PROTEIN  Length:416
 aligned with PNCB_AGRFC | Q8UIS9 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:426
                                    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       340       350       360       370       380       390       400       410       420      
           PNCB_AGRFC     1 MTKTDIATRVHNHTWKLDPIVRSLIDTDFYKLLMLQMIWKLYPEVDATFSLINRTKTVRLAEEIDEMELREQLDHARTLRLSKKENIWLAGNTFYGRSQIFEPEFLSWLSSYQLPEYELFKRDGQYELNFHGRWMDTTLWEIPALSIINELRSRSAMRSLGYFTLDVLYARAKAKMWEKVERLRELPGLRISDFGTRRRHSFLWQRWCVEALKEGIGPAFTGTSNVLLAMDSDLEAVGTNAHELPMVVAALAQTNEELAAAPYQVLKDWNRLYGGNLLIVLPDAFGTAAFLRNAPEWVADWTGFRPDSAPPIEGGEKIIEWWRKMGRDPRTKMLIFSDGLDVDAIVDTYRHFEGRVRMSFGWGTNLTNDFAGCAPKTIASLKPISIVCKVSDANGRPAVKLSDNPQKATGDPAEVERYLKFFGEED 426
               SCOP domains d1ybeb2 B     :8-167 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                                    d1ybeb1 B:168-433 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                                  SCOP domains
               CATH domains 1ybeB01 B     :8-416 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                                ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.-----.............hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhh......eeeeee..eeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......eee.......hhhhhhhhhhhhhhhhh..eeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhh.hhhhhhh.ee.....hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh.......-----.....ee..eeee..ee......hhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ybe B   8 MTKTDIATR-----WKLDPIVRSLIDTDFYKLLMLQMIWKLYPEVDATFSLINRTKTVRLAEEIDEMELREQLDHARTLRLSKKENIWLAGNTFYGRSQIFEPEFLSWLSSYQLPEYELFKRDGQYELNFHGRWMDTTLWEIPALSIINELRSRSAMRSLGYFTLDVLYARAKAKMWEKVERLRELPGLRISDFGTRRRHSFLWQRWCVEALKEGIGPAFTGTSNVLLAMDSDLEAVGTNAHELPMVVAALAQTNEELAAAPYQVLKDWNRLYGGNLLIVLPDAFGTAAFLRNAPEWVADWTGFRPDSAPPIEGGEKIIEWWRKMGRDPRTKMLIFSDGLDVDAIVDTYRHFEGRVRMSFGWGTNLTNDFAGCAP-----LKPISIVCKVSDANGRPAVKLSDNPQKATGDPAEVERYLKFFGEED 433
                                    |-    |   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       297       307       317       327       337       347       357       367       377    |    -|      397       407       417       427      
                                   16    22                                                                                                                                                                                                                                                                                                                                                                     382   388
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PNCB_AGRFC | Q8UIS9)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0004516    nicotinate phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate.
    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.
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:0019357    nicotinate nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid).
    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.

 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
(no "Ligands, Modified Residues, Ions" information available for 1ybe)
 
  Sites
(no "Sites" information available for 1ybe)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ybe)
 

(-) 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 ](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
  1ybe
    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
  PNCB_AGRFC | Q8UIS9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.11
    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
  PNCB_AGRFC | Q8UIS9
    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 1YBE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YBE)