Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF THE QUORUM-QUENCHING N-ACYL HOMOSERINE LACTONE HYDROLASE
 
Authors :  M. H. Kim, W. C. Choi, H. O. Kang, J. S. Lee, B. S. Kang, K. J. Kim, Z. S. Derewenda, T. K. Oh, C. H. Lee, J. K. Lee
Date :  03 Jun 05  (Deposition) - 07 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, N-Acyl Homoserine Lactone Hydrolase, Quorum Sensing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Kim, W. C. Choi, H. O. Kang, J. S. Lee, B. S. Kang, K. J. Kim, Z. S. Derewenda, T. K. Oh, C. H. Lee, J. K. Lee
The Molecular Structure And Catalytic Mechanism Of A Quorum-Quenching N-Acyl-L-Homoserine Lactone Hydrolase.
Proc. Natl. Acad. Sci. Usa V. 102 17606 2005
PubMed-ID: 16314577  |  Reference-DOI: 10.1073/PNAS.0504996102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AIIA-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-HIS-PARALLEL1/AIIA
    Expression System Strain: ESCHERICHIA COLI XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector: PMAL-HIS-PARALLEL1
    Organism Scientific: BACILLUS THURINGIENSIS
    Organism Taxid: 1428
    Synonym: ACYL-HOMOSERINE LACTONE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , HIS A:109 , ASP A:191 , HIS A:235 , ZN A:1252 , HOH A:2141 , HOH A:2142BINDING SITE FOR RESIDUE ZN A1251
2AC2SOFTWAREHIS A:104 , HIS A:106 , HIS A:169 , ASP A:191 , ZN A:1251 , HOH A:2104 , HOH A:2142BINDING SITE FOR RESIDUE ZN A1252
3AC3SOFTWAREHIS A:145 , LEU A:146 , LYS A:226 , HOH A:2082 , HOH A:2143BINDING SITE FOR RESIDUE GOL A1253
4AC4SOFTWAREMET A:-1 , HIS A:133 , PRO A:229 , ILE A:230 , ILE A:231 , HOH A:2001BINDING SITE FOR RESIDUE GOL A1254

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BTN)

(-) 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:242
 aligned with AHLLA_BACTK | P0CJ63 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:252
                              1                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  
          AHLLA_BACTK     - --MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.hhh........eeeeeeeeeeeee..eeeee....hhhh....----------.eeee.hhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh....eeeehhhhhhhh.....hhhhh.....eeee...eeee..eeeee........eeeeeee...eeeeeeehhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2btn A  -1 MDMTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNE----------QILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIKTEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
                                     8        18        28        38        48        58  |      -   |    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  
                                                                                         61         72                                                                                                                                                                                  


Chain A from PDB  Type:PROTEIN  Length:242
 aligned with AHLL_BACT3 | Q7B8C3 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:252
                              1                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  
           AHLL_BACT3     - --MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.hhh........eeeeeeeeeeeee..eeeee....hhhh....----------.eeee.hhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh....eeeehhhhhhhh.....hhhhh.....eeee...eeee..eeeee........eeeeeee...eeeeeeehhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2btn A  -1 MDMTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNE----------QILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIKTEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
                                     8        18        28        38        48        58  |      -   |    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  
                                                                                         61         72
   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 2BTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BTN)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AHLL_BACT3 | Q7B8C3)
molecular function
    GO:0102007    acyl-L-homoserine-lactone lactonohydrolase activity    Catalysis of the reaction: H2O + an N-acyl-L-homoserine lactone <=> H+ + an N-acyl-L-homoserine.
    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.

Chain A   (AHLLA_BACTK | P0CJ63)
molecular function
    GO:0102007    acyl-L-homoserine-lactone lactonohydrolase activity    Catalysis of the reaction: H2O + an N-acyl-L-homoserine lactone <=> H+ + an N-acyl-L-homoserine.
    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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:246 - Pro A:247   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2btn
    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
  AHLLA_BACTK | P0CJ63
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  AHLL_BACT3 | Q7B8C3
    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
  AHLLA_BACTK | P0CJ63
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  AHLL_BACT3 | Q7B8C3
    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
        AHLLA_BACTK | P0CJ63: 2a7m 2br6 3dha 3dhb 3dhc 5eh9
        AHLL_BACT3 | Q7B8C3: 2a7m 2br6

(-) Related Entries Specified in the PDB File

2a7m 1.6 ANGSTROM RESOLUTION STRUCTURE OF THE QUORUM-QUENCHING N-ACYL HOMOSERINE LACTONE HYDROLASE OF BACILLUS THURINGIENSIS
2br6 CRYSTAL STRUCTURE OF QUORUM-QUENCHING N-ACYL HOMOSERINE LACTONE LACTONASE