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(-) Description

Title :  N-ALKYLBORONIC ACID INHIBITORS REVEAL DETERMINANTS OF LIGAND SPECIFICITY IN THE QUORUM-QUENCHING AND SIDEROPHORE BIOSYNTHETIC ENZYME PVDQ
 
Authors :  R. Wu, K. D. Clevenger, W. Fast, D. Liu
Date :  03 Oct 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,C
Keywords :  N-Alkylboronic Acid Inhibitors Of Pvdq, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Clevenger, R. Wu, D. Liu, W. Fast
N-Alkylboronic Acid Inhibitors Reveal Determinants Of Ligan Specificity In The Quorum-Quenching And Siderophore Biosynthetic Enzyme Pvdq.
Biochemistry V. 53 6679 2014
PubMed-ID: 25290020  |  Reference-DOI: 10.1021/BI501086S

(-) Compounds

Molecule 1 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ
    Chains: C
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 217-762
    Gene: PVDQ, QSC112, PA2385
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: ACYL-HSL ACYLASE PVDQ
 
Molecule 2 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ
    Chains: A
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 28-192
    Gene: PVDQ, QSC112, PA2385
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: ACYL-HSL ACYLASE PVDQ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1BUB1Ligand/Ion1-BUTANE BORONIC ACID
2GOL18Ligand/IonGLYCEROL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER C:217 , HIS C:239 , THR C:285 , VAL C:286 , ASN C:485binding site for residue BUB C 801
02AC2SOFTWARELEU C:259 , ASP C:260 , ASN C:382 , ALA C:384 , GOL C:808binding site for residue GOL C 802
03AC3SOFTWAREILE A:101 , GLU C:336 , HIS C:337 , HOH C:901 , HOH C:907 , HOH C:1051binding site for residue GOL C 803
04AC4SOFTWAREGOL A:205 , TYR C:344 , GLY C:345 , LEU C:364 , ARG C:365 , ASP C:366 , LEU C:369 , HOH C:1072 , HOH C:1149binding site for residue GOL C 804
05AC5SOFTWAREARG C:365 , TRP C:455 , ALA C:464 , GLY C:465 , HOH C:904binding site for residue GOL C 805
06AC6SOFTWARETHR C:372 , ARG C:373 , ALA C:462 , HOH C:1067 , HOH C:1080 , HOH C:1093 , HOH C:1324binding site for residue GOL C 806
07AC7SOFTWAREPHE C:596 , ALA C:597 , LEU C:599 , ASP C:600 , GLY C:601 , ALA C:602 , TRP C:603binding site for residue GOL C 807
08AC8SOFTWAREGLY C:257 , ARG C:258 , ASP C:260 , GOL C:802binding site for residue GOL C 808
09AC9SOFTWAREALA C:470 , GLN C:498 , GLY C:499 , PHE C:500 , HOH C:1295binding site for residue GOL C 809
10AD1SOFTWAREASN C:485 , ASP C:486 , GLY C:511binding site for residue GOL C 810
11AD2SOFTWARELEU C:580 , ASP C:581 , ARG C:651 , ASP C:654 , ALA C:666binding site for residue GOL C 811
12AD3SOFTWAREPRO C:459 , ALA C:461 , HOH C:1290 , HOH C:1324 , HOH C:1375binding site for residue GOL C 812
13AD4SOFTWAREARG C:591 , ARG C:684 , HOH C:1104binding site for residue GOL C 813
14AD5SOFTWAREGLU A:172 , GLY A:173 , HOH A:462 , VAL C:286 , TRP C:402binding site for residue GOL A 201
15AD6SOFTWARELYS A:48 , ASP A:49 , LYS A:89 , GLU A:93 , LEU A:94 , ASP A:95 , ASP A:180binding site for residue GOL A 202
16AD7SOFTWARETRP A:116 , THR A:159 , ASP A:160 , HOH A:301 , HOH A:316 , HOH A:329 , LYS C:643binding site for residue GOL A 203
17AD8SOFTWAREPHE A:137 , ALA A:141 , ASP A:142 , GLY A:143 , LYS A:144 , THR A:145 , THR A:146 , HOH A:416binding site for residue GOL A 204
18AD9SOFTWARETRP A:105 , LEU A:106 , GLN A:108 , ARG A:167 , HOH A:446 , GOL C:804binding site for residue GOL A 205
19AE1SOFTWAREGLN A:177 , HOH A:404 , HOH A:457 , GLY C:442 , LEU C:443binding site for residue GOL A 206

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:148
2C:433 -C:453
3C:555 -C:568

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr C:615 -Pro C:616

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WKT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WKT)

(-) Exons   (0, 0)

(no "Exon" information available for 4WKT)

(-) 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeehhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkt A  28 PTGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAEK 192
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     


Chain C from PDB  Type:PROTEIN  Length:548
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeeee.eee.hhhhh.eeeeeee...eeeeeee........eee...eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeeeeee.....eeeeeeeeeee..ee.............eeeeeee.hhhh.hhhhhhhhhh...hhhhhhhhhhhhh....eeeeeee....eeee........hhhhhhhhhhhhhhhh...eee..hhhhh.............hhhhh.eeee..eeee...........................hhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee...........eee...hhhhhhhhhhhhhhhhhhhhhh......hhhhheeeee..eeee....hhhhh....eeeeee..eeeeeeee.eeeeee......eeeeee.............hhhhhhhhh...ee...hhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkt C 217 SNAIAVGSERSADGKGMLLANPHFPWNGAMRFYQMHLTIPGRLDVMGASLPGLPVVNIGFSRHLAWTHTVDTSSHFTLYRLALDPKDPRRYLVDGRSLPLEEKSVAIEVRGADGKLSRVEHKVYQSIYGPLVVWPGKLDWNRSEAYALRDANLENTRVLQQWYSINQASDVADLRRRVEALQGIPWVNTLAADEQGNALYMNQSVVPYLKPELIPACAIPQLVAEGLPALQGQDSRCAWSRDPAAAQAGITPAAQLPVLLRRDFVQNSNDSAWLTNPASPLQGFSPLVSQEKPIGPRARYALSRLQGKQPLEAKTLEEMVTANHVFSADQVLPDLLRLCRDNQGEKSLARACAALAQWDRGANLDSGSGFVYFQRFMQRFAELDGAWKEPFDAQRPLDTPQGIALDRPQVATQVRQALADAAAEVEKSGIPDGARWGDLQVSTRGQERIAIPGGDGHFGVYNAIQSVRKGDHLEVVGGTSYIQLVTFPEEGPKARGLLAFSQSSDPRSPHYRDQTELFSRQQWQTLPFSDRQIDADPQLQRLSIREAA 764
                                   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
   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 4WKT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WKT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WKT)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4wks 4wku 4wkv