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 PHENYLSERINE ALDOLASE FROM PSEUDOMONAS PUTIDA
 
Authors :  R. Omi
Date :  09 Dec 03  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Plp-Dependent Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Omi, I. Miyahara, H. Misono, K. Hirotsu
Crystal Structure Of Phenylserine Aldolase From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALDOLASE
    ChainsA
    EC Number4.1.2.26
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:163 , ASP A:167 , HIS A:341 , HOH A:719BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARETYR A:39 , THR A:67 , GLY A:68 , THR A:69 , HIS A:93 , THR A:148 , GLU A:152 , ASP A:179 , SER A:181 , ARG A:182 , LYS A:212 , SER A:244 , HOH A:544 , HOH A:599 , HOH A:642BINDING SITE FOR RESIDUE PLP A 513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V72)

(-) Exons   (0, 0)

(no "Exon" information available for 1V72)

(-) 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:345
 aligned with Q59IT3_PSEPU | Q59IT3 from UniProtKB/TrEMBL  Length:357

    Alignment length:345
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346     
         Q59IT3_PSEPU     7 RPPALGFSSDNIAGASPEVAQALVKHSSGQAGPYGTDELTAQVKRKFCEIFERDVEVFLVPTGTAANALCLSAMTPPWGNIYCHPASHINNDECGAPEFFSNGAKLMTVDGPAAKLDIVRLRERTREKVGDVHTTQPACVSITQATEVGSIYTLDEIEAIGDVCKSSSLGLHMDGSRFANALVSLGCSPAEMTWKAGVDALSFGATKNGVLAAEAIVLFNTSLATEMSYRRKRAGHLSSKMRFLSAQIDAYLTDDLWLRNARKANAAAQRLAQGLEGLGGVEVLGGTEANILFCRLDSAMIDALLKAGFGFYHDRWGPNVVRFVTSFATTAEDVDHLLNQVRLAA 351
               SCOP domains d1v72a1 A:6-350 Phenylserine aldolase PSALD                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Beta_elim_lyase-1v72A01 A:11-302                                                                                                                                                                                                                                                                    ------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..hhhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.....eeeee...hhhhhh..hhhhhhh...eeee..hhhhh.hhhhhhhhh..........eeeeeeee.........hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......hhhhh..eeee.hhhhh....eeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeeehhhhhhhhhhh............eeeee.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v72 A   6 RPPALGFSSDNIAGASPEVAQALVKHSSGQAGPYGTDELTAQVKRKFCEIFERDVEVFLVPTGTAANALCLSAMTPPWGNIYCHPASHINNDECGAPEFFSNGAKLMTVDGPAAKLDIVRLRERTREKVGDVHTTQPACVSITQATEVGSIYTLDEIEAIGDVCKSSSLGLHMDGSRFANALVSLGCSPAEMTWKAGVDALSFGATKNGVLAAEAIVLFNTSLATEMSYRRKRAGHLSSKMRFLSAQIDAYLTDDLWLRNARKANAAAQRLAQGLEGLGGVEVLGGTEANILFCRLDSAMIDALLKAGFGFYHDRWGPNVVRFVTSFATTAEDVDHLLNQVRLAA 350
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345     

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V72)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q59IT3_PSEPU | Q59IT3)
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: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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004793    threonine aldolase activity    Catalysis of the reaction: L-threonine = glycine + acetaldehyde.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

 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
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v72)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1v72
    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
  Q59IT3_PSEPU | Q59IT3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.2.26
    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
  Q59IT3_PSEPU | Q59IT3
    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 1V72)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V72)