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 :  STRUCTURAL STUDIES OF ADENYLOSUCCINATE LYASES
 
Authors :  E. A. Toth, T. Yeates
Date :  19 May 00  (Deposition) - 10 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Purine Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. A. Toth, C. Worby, J. E. Dixon, E. R. Goedken, S. Marqusee, T. O. Yeates
The Crystal Structure Of Adenylosuccinate Lyase From Pyrobaculum Aerophilum Reveals An Intracellular Protein With Three Disulfide Bonds.
J. Mol. Biol. V. 301 433 2000
PubMed-ID: 10926519  |  Reference-DOI: 10.1006/JMBI.2000.3970
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENYLOSUCCINATE LYASE
    ChainsA
    EC Number4.3.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPT7-7
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymASL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F1O)

(-) Sites  (0, 0)

(no "Site" information available for 1F1O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F1O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F1O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F1O)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.PUR8_BACSU261-270  1A:263-270

(-) Exons   (0, 0)

(no "Exon" information available for 1F1O)

(-) 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:351
 aligned with PUR8_BACSU | P12047 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:408
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408        
           PUR8_BACSU     9 EMSAIWTDENRFQAWLEVEILACEAWAELGVIPKEDVKVMRENASFDINRILEIEKDTRHDVVAFTRAVSESLGEERKWVHYGLTSTDVVDTALSYLLKQANDILLKDLERFVDIIKEKAKEHKYTVMMGRTHGVHAEPTTFGLKLALWHEEMKRNLERFKQAKAGIEVGKISGAVGTYANIDPFVEQYVCEKLGLKAAPISTQTLQRDRHADYMATLALIATSIEKFAVEIRGLQKSETREVEEFFAKGQKGSSAMPHKRNPIGSENMTGMARVIRGYMMTAYENVPLWHERDISHSSAERIILPDATIALNYMLNRFSNIVKNLTVFPENMKRNMDRTLGLIYSQRVLLALIDTGLTREEAYDTVQPKAMEAWEKQVPFRELVEAEEKITSRLSPEKIADCFDYNY 416
               SCOP domains d1f1oa_ A: Adenylosuccinate lyase                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................................................................................................................................--...........................................------..................................................................--------..................................................................................------..........-----------------------------------..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f1o A   9 EMSAIWTDENRFQAWLEVEILACEAWAELGVIPKEDVKVMRENASFDINRILEIEKDTRHDVVAFTRAVSESLGEERKWVHYGLTSTDVVDTALSYLLKQANDILLKDLERFVDIIKEKAKEHKYTVMM--THGVHAEPTTFGLKLALWHEEMKRNLERFKQAKAGIEVGKISG------NIDPFVEQYVCEKLGLKAAPISTQTLQRDRHADYMATLALIATSIEKFAVEIRGLQKSETREVEEF--------SAMPHKRNPIGSENMTGMARVIRGYMMTAYENVPLWHERDISHSSAERIILPDATIALNYMLNRFSNIVKNLTVFPENMKRN------LIYSQRVLLA-----------------------------------EEKITSRLSPEKIADCFDYNY 416
                                    18        28        38        48        58        68        78        88        98       108       118       128        |- |     148       158       168       178   |     -|      198       208       218       228       238       248     |   -    |  268       278       288       298       308       318       328       338     |   -  |    358 |       -         -         -       398       408        
                                                                                                                                                          137  |                                       182    189                                                              254      263                                                                              344    351      360                                 396                    
                                                                                                                                                             140                                                                                                                                                                                                                                                                                    

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1F1O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F1O)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUR8_BACSU | P12047)
molecular function
    GO:0070626    (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
    GO:0004018    N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity    Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0044208    'de novo' AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0009152    purine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

 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 1f1o)
 
  Sites
(no "Sites" information available for 1f1o)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f1o)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1f1o
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PUR8_BACSU | P12047
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.3.2.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PUR8_BACSU | P12047
    Protein Disorder PredictionDisEMBL | 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 1F1O)

(-) Related Entries Specified in the PDB File

1c3c 1c3u 1dof