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(-) Description

Title :  THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ WITH A COVALENTLY BOUND DODECANOIC ACID
 
Authors :  M. Bokhove, P. Nadal Jimenez, W. J. Quax, B. W. Dijkstra
Date :  16 Nov 09  (Deposition) - 29 Dec 09  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Zymogen, Hydrolase, Periplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bokhove, P. Nadal Jimenez, W. J. Quax, B. W. Dijkstra
The Quorum-Quenching N-Acyl Homoserine Lactone Acylase Pvdq Is An Ntn-Hydrolase With An Unusual Substrate-Binding Pocket
Proc. Natl. Acad. Sci. Usa V. 107 686 2010
PubMed-ID: 20080736  |  Reference-DOI: 10.1073/PNAS.0911839107

(-) Compounds

Molecule 1 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
    Atcc: 15692
    Chains: A
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCTNDE
    Expression System Strain: K-12 SUBSTR. DH10B
    Expression System Taxid: 316385
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Other Details: HOLLOWAY COLLECTION
    Strain: PAO1
    Synonym: ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA
 
Molecule 2 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
    Atcc: 15692
    Chains: B
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCTNDE
    Expression System Strain: K-12 SUBSTR. DH10B
    Expression System Taxid: 316385
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Other Details: HOLLOWAY COLLECTION
    Strain: PAO1
    Synonym: ACYL-HSL ACYLASE PVDQ SUBUNIT BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1DAO1Ligand/IonLAURIC ACID
2GOL6Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:1 , PHE B:24 , THR B:69 , VAL B:70 , VAL B:158 , TRP B:162 , ASN B:269 , HOH B:2222BINDING SITE FOR RESIDUE DAO B1547
2AC2SOFTWARELYS A:25 , ASP A:26 , GLU A:70 , LEU A:71 , ASP A:72 , ASP A:157BINDING SITE FOR RESIDUE GOL A1170
3AC3SOFTWARETHR B:156 , ARG B:157 , ALA B:246 , HOH B:2085 , HOH B:2088 , HOH B:2223BINDING SITE FOR RESIDUE GOL B1548
4AC4SOFTWAREGLN B:357 , TRP B:358 , ASP B:359 , ASP B:365 , GLY B:367BINDING SITE FOR RESIDUE GOL B1549
5AC5SOFTWAREGLU A:149 , GLY A:150 , GLN A:154 , MET B:30 , VAL B:70 , TRP B:186BINDING SITE FOR RESIDUE GOL A1171
6AC6SOFTWAREPRO B:40 , GLY B:41 , VAL B:119 , HIS B:121BINDING SITE FOR RESIDUE GOL B1550
7AC7SOFTWARELEU B:364 , ASP B:365 , ARG B:435 , GLY B:437 , ASP B:438BINDING SITE FOR RESIDUE GOL B1551

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:125
2B:217 -B:237
3B:339 -B:352

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:399 -Pro B:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WYB)

(-) 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:164
 aligned with PVDQ_PSEAE | Q9I194 from UniProtKB/Swiss-Prot  Length:762

    Alignment length:164
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           PVDQ_PSEAE    29 TGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAEK 192
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wyb A   6 TGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAEK 169
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    


Chain B from PDB  Type:PROTEIN  Length:546
 aligned with PVDQ_PSEAE | Q9I194 from UniProtKB/Swiss-Prot  Length:762

    Alignment length:546
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756      
           PVDQ_PSEAE   217 SNAIAVGSERSADGKGMLLANPHFPWNGAMRFYQMHLTIPGRLDVMGASLPGLPVVNIGFSRHLAWTHTVDTSSHFTLYRLALDPKDPRRYLVDGRSLPLEEKSVAIEVRGADGKLSRVEHKVYQSIYGPLVVWPGKLDWNRSEAYALRDANLENTRVLQQWYSINQASDVADLRRRVEALQGIPWVNTLAADEQGNALYMNQSVVPYLKPELIPACAIPQLVAEGLPALQGQDSRCAWSRDPAAAQAGITPAAQLPVLLRRDFVQNSNDSAWLTNPASPLQGFSPLVSQEKPIGPRARYALSRLQGKQPLEAKTLEEMVTANHVFSADQVLPDLLRLCRDNQGEKSLARACAALAQWDRGANLDSGSGFVYFQRFMQRFAELDGAWKEPFDAQRPLDTPQGIALDRPQVATQVRQALADAAAEVEKSGIPDGARWGDLQVSTRGQERIAIPGGDGHFGVYNAIQSVRKGDHLEVVGGTSYIQLVTFPEEGPKARGLLAFSQSSDPRSPHYRDQTELFSRQQWQTLPFSDRQIDADPQLQRLSIRE 762
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Penicil_amidase-2wybB01 B:1-539                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) Penicil_amidase-2wybB02 B:1-539                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author .eeeee..........eeeee.eee.hhhhh.eeeeeee...eeeeeee........eee...eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeeeeee.....eeeeeeeeeee..eeee...........eeeeeee.hhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeee....eeee........hhhhhhhhhhhhhhh....eee..hhhhh.............hhhhh.eeee..eeee...........................hhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee...........eee...hhhhhhhhhhhhhhhhhhhhhh......hhhhheeeee..eeee....hhhhh....eeeeee..eeeeeeee.eeeeee......eeeeee.............hhhhhhhhh...ee...hhhhhhhh...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wyb B   1 SNAIAVGSERSADGKGMLLANPHFPWNGAMRFYQMHLTIPGRLDVMGASLPGLPVVNIGFSRHLAWTHTVDTSSHFTLYRLALDPKDPRRYLVDGRSLPLEEKSVAIEVRGADGKLSRVEHKVYQSIYGPLVVWPGKLDWNRSEAYALRDANLENTRVLQQWYSINQASDVADLRRRVEALQGIPWVNTLAADEQGNALYMNQSVVPYLKPELIPACAIPQLVAEGLPALQGQDSRCAWSRDPAAAQAGITPAAQLPVLLRRDFVQNSNDSAWLTNPASPLQGFSPLVSQEKPIGPRARYALSRLQGKQPLEAKTLEEMVTANHVFSADQVLPDLLRLCRDNQGEKSLARACAALAQWDRGANLDSGSGFVYFQRFMQRFAELDGAWKEPFDAQRPLDTPQGIALDRPQVATQVRQALADAAAEVEKSGIPDGARWGDLQVSTRGQERIAIPGGDGHFGVYNAIQSVRKGDHLEVVGGTSYIQLVTFPEEGPKARGLLAFSQSSDPRSPHYRDQTELFSRQQWQTLPFSDRQIDADPQLQRLSIRE 546
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540
   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 2WYB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PVDQ_PSEAE | Q9I194)
molecular function
    GO:0009392    N-acetyl-anhydromuramoyl-L-alanine amidase activity    Catalysis of the reaction: GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-Ala + H2O glcNAc-1,6-anhMurNAc + L-Ala-gamma-D-Glu-DAP-D-Ala.
    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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009372    quorum sensing    The process in which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  3.5.1.97
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 Related Entries

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

UniProtKB/Swiss-Prot
        PVDQ_PSEAE | Q9I194: 2wyc 2wyd 2wye 3l91 3l94 3sra 3srb 3src 4bth 4k2f 4k2g 4m1j 4wks 4wkt 4wku 4wkv 5ubk 5ubl

(-) Related Entries Specified in the PDB File

2wyc THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IN COMPLEX WITH 3-OXO -LAURIC ACID
2wyd THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IN COMPLEX WITH DODECANOIC ACID
2wye THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IS AN NTN-HYDROLASE WITH AN UNUSUAL SUBSTRATE-BINDING POCKET