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(-) Description

Title :  AN ULTRAL HIGH RESOLUTION STRUCTURE OF N-ACYL HOMOSERINE LACTONE HYDROLASE WITH THE PRODUCT N-HEXANOYL-L-HOMOSERINE BOUND AT AN ALTERNATIVE SITE
 
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 :  0.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Bimetallohydrolase, Quorum Quenching, N-Acyl Homoserine Lactone, Alternative Binding Site, Product Complex, Ahl Lactonase, 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 BEFORE CRYSTALLIZATION USING TEV PROTEASE RESULTING IN 4 EXTRA RESIDUES AT THE N TERMINUS.
    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, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1C6L1Ligand/IonN-HEXANOYL-L-HOMOSERINE
2GOL4Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:112 , HIS A:113 , ASP A:195 , HIS A:239 , HOH A:307BINDING SITE FOR RESIDUE ZN A 255
2AC2SOFTWAREHIS A:108 , HIS A:110 , HIS A:173 , ASP A:195 , HOH A:307BINDING SITE FOR RESIDUE ZN A 256
3AC3SOFTWARESER A:24 , PHE A:72 , GLN A:76 , ILE A:77 , HIS A:110 , PHE A:111 , GLU A:140 , TYR A:198 , HOH A:290 , HOH A:300 , HOH A:326 , HOH A:447 , HOH A:466BINDING SITE FOR RESIDUE C6L A 257
4AC4SOFTWARELEU A:34 , ARG A:93 , PHE A:250 , HOH A:344 , HOH A:394BINDING SITE FOR RESIDUE GOL A 258
5AC5SOFTWAREPRO A:98 , ALA A:119 , THR A:130 , GLY A:157 , TYR A:169 , HOH A:264 , HOH A:306 , HOH A:389 , HOH A:513BINDING SITE FOR RESIDUE GOL A 259
6AC6SOFTWAREMET A:57 , GLU A:59 , ILE A:87 , GLY A:115 , ALA A:119 , GLU A:156 , HOH A:270 , HOH A:316 , HOH A:348 , HOH A:357 , HOH A:433BINDING SITE FOR RESIDUE GOL A 260
7AC7SOFTWAREHIS A:149 , LEU A:150 , ASN A:151 , LYS A:230 , HOH A:304 , HOH A:327 , HOH A:342 , HOH A:482BINDING SITE FOR RESIDUE GOL A 261

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:250 -Pro A:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DHA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DHA)

(-) 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:254
 aligned with AHLLA_BACTK | P0CJ63 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:254
                                1                                                                                                                                                                                                                                                         
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    
          AHLLA_BACTK     - ----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....eeeehhhhhhhhhh...hhhhh.....eeee...eeee..eeeee........eeeeeee...eeeeeeehhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dha A   1 GRISMTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 254
                                    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:254
 aligned with AHLL_BACTU | A3FJ64 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:254
                                1                                                                                                                                                                                                                                                         
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    
           AHLL_BACTU     - ----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....eeeehhhhhhhhhh...hhhhh.....eeee...eeee..eeeee........eeeeeee...eeeeeeehhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dha A   1 GRISMTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 254
                                    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)
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  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 3DHA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AHLLA_BACTK | P0CJ63: 2a7m 2br6 2btn 3dhb 3dhc 5eh9
        AHLL_BACTU | A3FJ64: 3dhb 3dhc 4j5f 4j5h 5eht

(-) Related Entries Specified in the PDB File

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