Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS PUTATIVE NICOTINATE PHOSPHORIBOSYLTRANSFERASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
 
Authors :  Y. Patskovsky, S. C. Almo, S. K. Burley, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  30 Nov 05  (Deposition) - 13 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. C. Almo
Crystal Structure Of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE, PUTATIVE
    Chains: A
    EC Number: 2.4.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF2626
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3NIO2Ligand/IonNICOTINIC ACID
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1DPO2Ligand/IonDIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3NIO4Ligand/IonNICOTINIC ACID
4SO416Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:69 , GLU A:70 , HOH A:856BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASN A:293 , ASP A:294 , GLY A:316 , THR A:317 , HOH A:835 , HOH A:1034BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREHIS A:225 , ARG A:226 , ASP A:227 , HOH A:847 , HOH A:1059BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREARG A:226 , ASN A:257BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREARG A:276 , THR A:285 , GLU A:286 , ALA A:287 , LYS A:288 , ASP A:311 , SER A:372 , HOH A:914 , HOH A:1175BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWAREILE A:194 , PHE A:195 , SO4 A:510 , HOH A:1121BINDING SITE FOR RESIDUE SO4 A 507
07AC7SOFTWAREALA A:6 , ASP A:7 , SO4 A:507BINDING SITE FOR RESIDUE SO4 A 510
08AC8SOFTWAREARG A:426 , GLU A:429 , LEU A:430BINDING SITE FOR RESIDUE SO4 A 511
09AC9SOFTWAREASP A:15 , TYR A:17 , PHE A:160 , ARG A:163 , GLY A:201 , THR A:202 , ARG A:262 , HOH A:809BINDING SITE FOR RESIDUE NIO A 601
10BC1SOFTWAREMET A:396 , HIS A:398 , ILE A:404 , LYS A:406 , PRO A:461 , ASP A:463 , HOH A:865 , HOH A:1168BINDING SITE FOR RESIDUE NIO A 602
11BC2SOFTWARETYR A:17 , ARG A:163 , ALA A:204 , HIS A:205 , SER A:206 , ARG A:262 , ASP A:264 , PHE A:332 , LYS A:333 , HOH A:818 , HOH A:875BINDING SITE FOR RESIDUE DPO A 701
12BC3SOFTWAREGLU A:38 , TYR A:40 , GLU A:112 , PRO A:113 , THR A:359 , LYS A:363 , HOH A:976BINDING SITE FOR RESIDUE GOL A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F7F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:4 -Tyr A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F7F)

(-) Exons   (0, 0)

(no "Exon" information available for 2F7F)

(-) 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:482
 aligned with Q830Y8_ENTFA | Q830Y8 from UniProtKB/TrEMBL  Length:494

    Alignment length:482
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483  
         Q830Y8_ENTFA     4 TYADDSLTLHTDMYQINMMQTYWELGRADLHAVFECYFREMPFNHGYAIFAGLERLVNYLENLTFTESDIAYLREVEEYPEDFLTYLANFEFKCTVRSALEGDLVFNNEPLIQIEGPLAQCQLVETALLNMVNFQTLIATKAARIKSVIGDDPLLEFGTRRAQELDAAIWGTRAAYIGGADATSNVRAGKIFGIPVSGTHAHSLVQSYGNDYEAFMAYAKTHRDCVFLVDTYDTLKAGVPSAIRVAREMGDKINFLGVRIDSGDMAYISKRVREQLDEAGFTEAKIYASNDLDENTILNLKMQKSKIDVWGVGTKLITAYDQPALGAVFKLVSIEGEDGQMKDTIKLSSNAEKVTTPGKKQVWRITRKSDKKSEGDYVTLWNEDPRQEEEIYMFHPVHTFINKYVRDFEARPVLQDIFVEGKRVYELPTLDEIKQYAKENLDSLWEEYKRDLNPQKYPVDLSTDCWNHKMNLLEKVRKDVKH 485
               SCOP domains d2f7fa2 A:4-140 Putative nicotinate phosphoribosyltransferase EF2626                                                                     d2f7fa1 A:141-485 Putative nicotinate phosphoribosyltransferase EF2626                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh.....eeeeeee...hhhhh..ee..hhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhh.....eeee.....ee......eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh..ee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhheeeeeee...hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....eeeehhhhhh.........eeeeeeee.....eee................eeeeeeee.....eeeeeeee...hhhhh.eeeee.......eeeee.eeeee..eeeee..ee.....hhhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f7f A   4 TYADDSLTLHTDMYQINMMQTYWELGRADLHAVFECYFREMPFNHGYAIFAGLERLVNYLENLTFTESDIAYLREVEEYPEDFLTYLANFEFKCTVRSALEGDLVFNNEPLIQIEGPLAQCQLVETALLNMVNFQTLIATKAARIKSVIGDDPLLEFGTRRAQELDAAIWGTRAAYIGGADATSNVRAGKIFGIPVSGTHAHSLVQSYGNDYEAFMAYAKTHRDCVFLVDTYDTLKAGVPSAIRVAREMGDKINFLGVRIDSGDMAYISKRVREQLDEAGFTEAKIYASNDLDENTILNLKMQKSKIDVWGVGTKLITAYDQPALGAVFKLVSIEGEDGQMKDTIKLSSNAEKVTTPGKKQVWRITRKSDKKSEGDYVTLWNEDPRQEEEIYMFHPVHTFINKYVRDFEARPVLQDIFVEGKRVYELPTLDEIKQYAKENLDSLHEEYKRDLNPQKYPVDLSTDCWNHKMNLLEKVRKDVKH 485
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483
   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, 2)

Asymmetric 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 2F7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F7F)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q830Y8_ENTFA | Q830Y8)
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.
    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: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:0019358    nicotinate nucleotide salvage    The generation of nicotinate nucleotide without de novo synthesis.
    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 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
    DPO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NIO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:4 - Tyr A:5   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2f7f
    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
  Q830Y8_ENTFA | Q830Y8
    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)
  2.4.2.11
    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
  Q830Y8_ENTFA | Q830Y8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q830Y8_ENTFA | Q830Y8: 4mzy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2F7F)