Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - 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 Asym.Unit - manually
Asym.Unit - 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 PHOSPHONOPYRUVATE HYDROLASE
 
Authors :  C. C. H. Chen, O. Herzberg
Date :  20 Jul 06  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Phosphonopyruvate Hydrolase, Phosphorus-Carbon Bond Cleavage, Phosphonopyruvate, Pep Mutase/Isocitrate Lyase Superfamily, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. H. Chen, Y. Han, W. Niu, A. N. Kulakova, A. Howard, J. P. Quinn, D. Dunaway-Mariano, O. Herzberg
Structure And Kinetics Of Phosphonopyruvate Hydrolase From Voriovorax Sp. Pal2: New Insight Into The Divergence Of Catalysis Within The Pep Mutase/Isocitrate Lyase Superfamil
Biochemistry V. 45 11491 2006
PubMed-ID: 16981709  |  Reference-DOI: 10.1021/BI061208L

(-) Compounds

Molecule 1 - PHOSPHONOPYRUVATE HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PPHA
    Organism Scientific: VARIOVORAX SP.
    Organism Taxid: 218557
    Strain: PAL2

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:23 , SER A:49 , CL A:376 , CL A:472BINDING SITE FOR RESIDUE NA A 309
2AC2SOFTWAREMET A:66 , NA A:309 , HOH A:371BINDING SITE FOR RESIDUE CL A 376
3AC3SOFTWAREHIS A:23 , ASN A:24 , NA A:309BINDING SITE FOR RESIDUE CL A 472

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:114 -Pro A:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HRW)

(-) 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:281
 aligned with PPHA_VARSP | Q84G06 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:290
                                    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
           PPHA_VARSP     1 MTKNQALRAALDSGRLFTAMAAHNPLVAKLAEQAGFGGIWGSGFELSASYAVPDANILSMSTHLEMMRAIASTVSIPLIADIDTGFGNAVNVHYVVPQYEAAGASAIVMEDKTFPKDTSLRTDGRQELVRIEEFQGKIAAATAARADRDFVVIARVEALIAGLGQQEAVRRGQAYEEAGADAILIHSRQKTPDEILAFVKSWPGKVPLVLVPTAYPQLTEADIAALSKVGIVIYGNHAIRAAVGAVREVFARIRRDGGIREVDAALPSVKEIIELQGDERMRAVEARYLK 290
               SCOP domains d2hrwa_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2hrwA00 A:1-290 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..eeeehhhhhhhhh........hhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhh..eeeee......---------....hhhhhhhhhhhhhhhh.....eeeeeehhhhhh.hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhh.....eee........hhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hrw A   1 MTKNQALRAALDSGRLFTAMAAHNPLVAKLAEQAGFGGIWGSGFELSASYAVPDANILSMSTHLEMMRAIASTVSIPLIADIDTGFGNAVNVHYVVPQYEAAGASAIVMEDKTFPK---------QELVRIEEFQGKIAAATAARADRDFVVIARVEALIAGLGQQEAVRRGQAYEEAGADAILIHSRQKTPDEILAFVKSWPGKVPLVLVPTAYPQLTEADIAALSKVGIVIYGNHAIRAAVGAVREVFARIRRDGGIREVDAALPSVKEIIELQGDERMRAVEARYLK 290
                                    10        20        30        40        50        60        70        80        90       100       110     |   -     | 130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
                                                                                                                                             116       126
   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 2HRW)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (PPHA_VARSP | Q84G06)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0033978    phosphonopyruvate hydrolase activity    Catalysis of the reaction: 3-phosphonopyruvate + H(2)O = phosphate + pyruvate.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:114 - Pro A:115   [ 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
  2hrw
    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
  PPHA_VARSP | Q84G06
    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)
  (no 'Enzyme Classificator' available)
    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
  PPHA_VARSP | Q84G06
    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
        PPHA_VARSP | Q84G06: 2dua 2hjp

(-) Related Entries Specified in the PDB File

2dua CRYSTAL STRUCTURE OF PHOSPHONOPYRUVATE HYDROLASE COMPLEX WITH OXALATE AND MG++
2hjp CRYSTAL STRUCTURE OF PHOSPHONOPYRUVATE HYDROLASE COMPLEX WITH PHOSPHONOPYRUVATE AND MG++