Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 ADENINE PHOSPHORIBOSYLTRANSFERASE
 
Authors :  W. Shi, K. S. E. Tanaka, S. C. Almo, V. L. Schramm
Date :  20 Oct 00  (Deposition) - 05 Dec 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dimer, Catalytic Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Shi, K. S. Tanaka, T. R. Crother, M. W. Taylor, S. C. Almo, V. L. Schram
Structural Analysis Of Adenine Phosphoribosyltransferase From Saccharomyces Cerevisiae.
Biochemistry V. 40 10800 2001
PubMed-ID: 11535055  |  Reference-DOI: 10.1021/BI010465H

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE 1
    Chains: A
    EC Number: 2.4.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:133 , THR A:134 , GLY A:135 , GLY A:136 , SER A:137 , HOH A:516 , HOH A:540BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLU A:67 , SER A:68 , ARG A:69 , ARG A:89 , LYS A:90 , LYS A:93 , HOH A:533BINDING SITE FOR RESIDUE SO4 A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G2P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:67 -Ser A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G2P)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT1_YEAST125-137  1A:125-137
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT1_YEAST125-137  2A:125-137

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YML022W1YML022W.1XIII:228937-229500564APT1_YEAST1-1871871A:5-178 (gaps)174

(-) 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:170
 aligned with APT1_YEAST | P49435 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
           APT1_YEAST     5 SYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
               SCOP domains d1g2pa_ A: Adenine PRTase                                                                                                                                                      SCOP domains
               CATH domains 1g2pA00 A:5-178  [code=3.40.50.2020, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhheee.........eeehhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.eeeeeee.......eeeeee.----.eeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR----------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-178 (gaps) UniProt: 1-187 [INCOMPLETE]                                                                                                                      Transcript 1
                 1g2p A   5 SYAQELKLALHQYPNFPSEGILFEDFLPIFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLESRGFLFGPTLALALGVGFVPVRKAGKLPGECFKATYE----SDLFEIQKNAIPAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMELDFLKGRSKLNAPVFTLL 178
                                    14        24        34        44        54        64        74        84        94       104    |  114       124       134       144       154       164       174    
                                                                                                                             104  109
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G2P)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (APT1_YEAST | P49435)
molecular function
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:67 - Ser A:68   [ 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
  1g2p
    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
  APT1_YEAST | P49435
    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)
  2.4.2.7
    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
  APT1_YEAST | P49435
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        APT1_YEAST | P49435: 1g2q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1G2P)