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 :  APO CLASS II ALDOLASE HPCH
 
Authors :  D. Rea, V. Fulop, T. D. H. Bugg, D. I. Roper
Date :  05 Jul 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Lyase, Class Ii Aldolase, Homoprotocatechuate, Aromatic Degradation, Aromatic Hydrocarbons Catabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Rea, V. Fulop, T. D. H. Bugg, D. I. Roper
Structure And Mechanism Of Hpch: A Metal Ion Dependent Class Ii Aldolase From The Homoprotocatechuate Degradation Pathway Of Escherichia Coli.
J. Mol. Biol. V. 373 866 2007
PubMed-ID: 17881002  |  Reference-DOI: 10.1016/J.JMB.2007.06.048

(-) Compounds

Molecule 1 - 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: PPROEX-HTA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 498388
    Strain: C
    Synonym: HHED ALDOLASE, 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
1GOL15Ligand/IonGLYCEROL
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:6 , LYS A:10 , ARG A:109 , GLU A:164 , GLY A:165 , ASP A:167BINDING SITE FOR RESIDUE PO4 A1260
2AC2SOFTWARELYS B:6 , LYS B:10 , ARG B:109 , GLU B:164 , ASP B:167 , HOH B:2141BINDING SITE FOR RESIDUE PO4 B1253
3AC3SOFTWARESER A:24 , SER A:25 , TYR A:26 , HOH A:2031 , HOH A:2266 , SER B:23 , GLN B:51 , LEU B:54 , GOL B:1254BINDING SITE FOR RESIDUE GOL A1261
4AC4SOFTWARESER A:23 , GLN A:51 , LEU A:54 , GOL A:1261 , SER B:24 , SER B:25 , TYR B:26 , HOH B:2035 , HOH B:2037BINDING SITE FOR RESIDUE GOL B1254
5AC5SOFTWAREALA A:0 , GLY A:86 , GLN A:88 , ALA A:125 , ARG A:127 , HOH A:2167 , HOH A:2267 , HOH A:2268BINDING SITE FOR RESIDUE GOL A1262
6AC6SOFTWAREALA B:0 , GLY B:86 , GLN B:88 , ALA B:125 , ARG B:127 , HOH B:2242BINDING SITE FOR RESIDUE GOL B1255
7AC7SOFTWARELEU A:9 , LYS A:10 , ARG A:203 , GLY A:206 , HOH A:2198 , HOH A:2269BINDING SITE FOR RESIDUE GOL A1263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V5J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:111 -Pro A:112
2Pro B:111 -Pro B:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V5J)

(-) Exons   (0, 0)

(no "Exon" information available for 2V5J)

(-) 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:269
 aligned with HPCH_ECOLX | Q47098 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:269
                                     1                                                                                                                                                                                                                                                                   
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         
           HPCH_ECOLX     - ---------MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQATAVKPG 260
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh........hhhhh.hhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v5j A  -8 TENLYFQGAMENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQATAVKPG 260
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with HPCH_ECOLX | Q47098 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                     1                                                                                                                                                                                                                                                            
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  
           HPCH_ECOLX     - ---------MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQ 253
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------HpcH_HpaI-2v5jB01 B:15-242                                                                                                                                                                                                          ----------- Pfam domains (1)
           Pfam domains (2) -----------------------HpcH_HpaI-2v5jB02 B:15-242                                                                                                                                                                                                          ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh.hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh........hhhhh.hhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v5j B  -8 TENLYFQGAMENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGAQ 253
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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  (0, 0)

(no "SCOP Domain" information available for 2V5J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V5J)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HPCH_ECOLX | Q47098)
molecular function
    GO:0018802    2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity    Catalysis of the reaction: 2,4-dihydroxy-hept-trans-2-ene-1,7-dioate = pyruvate + succinic semialdehyde.
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0010124    phenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylacetate.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
    Pro A:111 - Pro A:112   [ RasMol ]  
    Pro B:111 - Pro B:112   [ 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
  2v5j
    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
  HPCH_ECOLX | Q47098
    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)
  4.1.2.-
    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
  HPCH_ECOLX | Q47098
    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
        HPCH_ECOLX | Q47098: 2v5k

(-) Related Entries Specified in the PDB File

2v5k CLASS II ALDOLASE HPCH - MAGNESIUM - OXAMATE COMPLEX