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 :  1.4 ANGSTROM STRUCTURE OF N-ACYL HOMOSERINE LACTONE HYDROLASE WITH THE PRODUCT N-HEXANOYL-L-HOMOSERINE BOUND AT THE CATALYTIC METAL CENTER
 
Authors :  D. Liu, J. Momb, P. W. Thomas, A. Moulin, G. A. Petsko, W. Fast, D. Ringe
Date :  17 Jun 08  (Deposition) - 29 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Bimetallohydrolase, Qourum Quenching, N-Acyl Homoserine Lactone, Product Complex, Ahl Lactonase, General Acid, Catalytic Mechanism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Liu, J. Momb, P. W. Thomas, A. Moulin, G. A. Petsko, W. Fast, D. Ringe
Mechanism Of The Quorum-Quenching Lactonase (Aiia) From Bacillus Thuringiensis. 1. Product-Bound Structures.
Biochemistry V. 47 7706 2008
PubMed-ID: 18627129  |  Reference-DOI: 10.1021/BI800368Y
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ACYL HOMOSERINE LACTONE HYDROLASE
    Chains: A
    EC Number: 3.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: AIIA
    Organism Scientific: BACILLUS THURINGIENSIS SEROVAR KURSTAKI
    Organism Taxid: 29339
    Other Details: THE FUSION PROTEIN, MALTOSE BINDING PROTEIN, WAS CUT OFF USING TEV PROTEASE RESULTING 4 EXTRA RESIDUES AT THE N TERMINUS IN THE SEQUENCE. BUT THE EXTRA RESIDUES ARE NOT SEEN IN THE STRUCTURE.
    Synonym: AIIA-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1C6L1Ligand/IonN-HEXANOYL-L-HOMOSERINE
2GOL7Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:108 , HIS A:109 , ASP A:191 , HIS A:235BINDING SITE FOR RESIDUE ZN A 251
02AC2SOFTWAREHIS A:104 , HIS A:106 , HIS A:169 , ASP A:191BINDING SITE FOR RESIDUE ZN A 252
03AC3SOFTWARELEU A:16 , HIS A:104 , HIS A:106 , PHE A:107 , ASP A:108 , HIS A:109 , HIS A:169 , ASP A:191 , TYR A:194 , GLY A:207 , PHE A:208 , HIS A:235 , HOH A:309 , HOH A:411BINDING SITE FOR RESIDUE C6L A 253
04AC4SOFTWARELYS A:29 , LEU A:30 , ARG A:89 , PHE A:246 , HOH A:310 , HOH A:363BINDING SITE FOR RESIDUE GOL A 254
05AC5SOFTWAREALA A:115 , THR A:126 , GLU A:152 , GLY A:153 , HOH A:277 , HOH A:279 , HOH A:407 , HOH A:476 , HOH A:477BINDING SITE FOR RESIDUE GOL A 255
06AC6SOFTWAREHIS A:145 , LYS A:226 , HOH A:311 , HOH A:457 , HOH A:513 , HOH A:530BINDING SITE FOR RESIDUE GOL A 256
07AC7SOFTWAREGLU A:61 , GLY A:62 , ASN A:65 , LEU A:74 , TYR A:249BINDING SITE FOR RESIDUE GOL A 257
08AC8SOFTWAREARG A:13 , ASN A:32 , GLU A:41 , LYS A:76 , TYR A:92 , HOH A:329 , HOH A:458 , HOH A:533BINDING SITE FOR RESIDUE GOL A 258
09AC9SOFTWAREMET A:53 , GLU A:55 , ILE A:83 , GLY A:111 , GLY A:112 , ALA A:115 , GLU A:152 , HOH A:273 , HOH A:285 , HOH A:321 , HOH A:340 , HOH A:481BINDING SITE FOR RESIDUE GOL A 259
10BC1SOFTWAREASN A:59 , ASN A:60 , GLU A:61 , LYS A:76 , MET A:77 , HOH A:295 , HOH A:443 , HOH A:458BINDING SITE FOR RESIDUE GOL A 260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DHB)

(-) 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 3DHB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DHB)

(-) Exons   (0, 0)

(no "Exon" information available for 3DHB)

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

    Alignment length:250
                                    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
          AHLLA_BACTK     1 MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee.hhh........eeeeeeeeeeeee..eeeee....hhhhh..............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
                 3dhb A   1 MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
                                    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


Chain A from PDB  Type:PROTEIN  Length:250
 aligned with AHLL_BACTU | A3FJ64 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    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
           AHLL_BACTU     1 MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee.hhh........eeeeeeeeeeeee..eeeee....hhhhh..............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
                 3dhb A   1 MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
                                    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
   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 3DHB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DHB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DHB)

(-) Gene Ontology  (4, 7)

Asymmetric/Biological Unit(hide GO term definitions)
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.

Chain A   (AHLL_BACTU | A3FJ64)
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.
biological process
    GO:1901335    lactone catabolic process    The chemical reactions and pathways resulting in the breakdown of lactone.

 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
    C6L  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ 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
  3dhb
    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_BACTU | A3FJ64
    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)
  3.1.1.-
    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_BACTU | A3FJ64
    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 2btn 3dha 3dhc 5eh9
        AHLL_BACTU | A3FJ64: 3dha 3dhc 4j5f 4j5h 5eht

(-) Related Entries Specified in the PDB File

2a7m THE SAME PROTEIN WITHOUT PRODUCT BOUND TO THE ACTIVE SITE.
2r2d A HOMOLOG PROTEIN FROM AGRABACTERIUM TUMEFACIENS
3dha N-ACYL HOMOSERINE LACTONE HYDROLASE WITH N-HEXANOYL-L- HOMOSERINE
3dhc N-ACYL HOMOSERINE LACTONE HYDROLASE WITH N-HEXANOYL-L- HOMOCYSTEINE