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(-) Description

Title :  1.3 ANGSTROM STRUCTURE OF N-ACYL HOMOSERINE LACTONE HYDROLASE WITH THE PRODUCT N-HEXANOYL-L-HOMOCYSTEINE BOUND TO 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 :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Bimetallohydrolase, Qourum Quenching, N-Acyl Homocysteine Thiolactone, 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: TEV PROTEASE WAS USED TO CUT OFF THE FUSION PROTEIN MBP RESULTING IN 4 EXTRA RESIDUES AT THE N TERMINUS. THE EXTRA RESIDUES ARE NOT OBSERVED 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, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CYK1Ligand/IonN-HEXANOYL-L-HOMOCYSTEINE
2GOL6Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:104 , HIS A:106 , HIS A:169 , ASP A:191 , ZN A:252 , CYK A:253BINDING SITE FOR RESIDUE ZN A 251
2AC2SOFTWAREASP A:108 , HIS A:109 , ASP A:191 , HIS A:235 , ZN A:251 , CYK A:253BINDING SITE FOR RESIDUE ZN A 252
3AC3SOFTWARELEU A:16 , HIS A:106 , PHE A:107 , ASP A:108 , HIS A:109 , HIS A:169 , ASP A:191 , TYR A:194 , HIS A:235 , ZN A:251 , ZN A:252 , HOH A:442 , HOH A:501BINDING SITE FOR RESIDUE CYK A 253
4AC4SOFTWAREASN A:59 , ASN A:60 , GLU A:61 , LYS A:76 , MET A:77 , HOH A:278 , HOH A:360BINDING SITE FOR RESIDUE GOL A 254
5AC5SOFTWARELYS A:29 , LEU A:30 , ARG A:89 , PHE A:246 , HOH A:310 , HOH A:332BINDING SITE FOR RESIDUE GOL A 255
6AC6SOFTWAREGLU A:61 , GLY A:62 , ASN A:65 , PRO A:247BINDING SITE FOR RESIDUE GOL A 256
7AC7SOFTWAREMET A:53 , GLU A:55 , GLY A:111 , ALA A:115 , GLU A:152 , HOH A:267 , HOH A:293 , HOH A:329 , HOH A:471BINDING SITE FOR RESIDUE GOL A 257
8AC8SOFTWAREHIS A:133 , ARG A:134 , PRO A:171 , SER A:242 , HOH A:306 , HOH A:455 , HOH A:520BINDING SITE FOR RESIDUE GOL A 258
9AC9SOFTWAREPRO A:94 , ALA A:115 , GLU A:152 , HOH A:290 , HOH A:295 , HOH A:408BINDING SITE FOR RESIDUE GOL A 259

(-) SS Bonds  (0, 0)

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

(-) 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 3DHC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DHC)

(-) 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
                 3dhc 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
                 3dhc 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)
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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 3DHC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3dha 3dhb 5eh9
        AHLL_BACTU | A3FJ64: 3dha 3dhb 4j5f 4j5h 5eht

(-) Related Entries Specified in the PDB File

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