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(-) Description

Title :  STRUCTURE OF PSEUDOMONAS AERUGINOSA PVDQ BOUND TO SMER28
 
Authors :  A. M. Gulick, E. J. Drake
Date :  07 Jul 11  (Deposition) - 21 Sep 11  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nrps Tailoring, Acylase, Liganded, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Drake, A. M. Gulick
Structural Characterization And High-Throughput Screening O Inhibitors Of Pvdq, An Ntn Hydrolase Involved In Pyoverdine Synthesis.
Acs Chem. Biol. V. 6 1277 2011
PubMed-ID: 21892836  |  Reference-DOI: 10.1021/CB2002973

(-) Compounds

Molecule 1 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ
    Chains: A
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PED485
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET15BTEV
    Fragment: ALPHA SUBUNIT (UNP RESIDUES 29-191)
    Gene: PA2385, PA2385 PVDQ, QSC112
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: AHL ACYLASE PVDQ, ACYL-HSL ACYLASE PVDQ
 
Molecule 2 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ
    Chains: B
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PED485
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET15BTEV
    Fragment: BETA SUBUNIT (UNP RESIDUES 217-762)
    Gene: PA2385, PA2385 PVDQ, QSC112
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: AHL ACYLASE PVDQ, ACYL-HSL ACYLASE PVDQ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
128S1Ligand/Ion6-BROMO-N-(PROP-2-EN-1-YL)QUINAZOLIN-4-AMINE
2EDO9Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:77 , GLU A:79 , HOH A:221 , HOH A:222 , HOH A:242 , HOH A:545BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWARELYS A:48 , GLU A:93 , LEU A:94 , ASP A:95 , ASP A:180BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREILE A:101 , VAL A:183 , HOH A:213 , HOH A:475 , HIS B:337BINDING SITE FOR RESIDUE EDO A 8
04AC4SOFTWAREALA A:111 , PHE A:115 , ARG A:167 , LEU B:369 , THR B:372BINDING SITE FOR RESIDUE EDO A 9
05AC5SOFTWAREHOH A:12 , ALA A:47 , LYS A:48 , ALA A:184 , HOH A:474 , HOH A:496 , PRO B:256 , PRO B:351BINDING SITE FOR RESIDUE EDO A 10
06AC6SOFTWAREALA A:92 , TYR A:103 , ARG A:168 , GLU A:172 , HOH A:238 , HOH A:509 , HOH A:554 , ALA B:245 , MET B:246BINDING SITE FOR RESIDUE SO4 A 192
07AC7SOFTWARELEU B:259 , ASP B:260 , ASN B:382BINDING SITE FOR RESIDUE EDO B 3
08AC8SOFTWAREPHE B:596 , ALA B:597 , LEU B:599 , GLY B:601 , ALA B:602 , TRP B:603BINDING SITE FOR RESIDUE EDO B 5
09AC9SOFTWAREGLN B:573 , TRP B:574 , ASP B:575 , ASP B:581 , GLY B:583BINDING SITE FOR RESIDUE EDO B 6
10BC1SOFTWARELEU B:308 , GLY B:311 , ASP B:729 , GLU B:732 , HOH B:817 , HOH B:948BINDING SITE FOR RESIDUE EDO B 7
11BC2SOFTWARELEU A:169 , LEU A:170 , LEU B:269 , VAL B:271 , ASN B:273 , VAL B:374 , LEU B:375 , TRP B:378 , TRP B:402 , HOH B:866BINDING SITE FOR RESIDUE 28S B 1

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SRB)

(-) 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:163
 aligned with PVDQ_PSEAE | Q9I194 from UniProtKB/Swiss-Prot  Length:762

    Alignment length:163
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
           PVDQ_PSEAE    29 TGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAE 191
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh..hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3srb A  29 TGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAE 191
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   


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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..........eeeee.eee.hhhhh.eeeeeee...eeeeeee........eee...eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeeeeee.....eeeeeeeeeee..ee.............eeeeeee.hhhh.hhhhhhhhhhh..hhhhhhhhhhhhh....eeeeeee....eeee........hhhhhhhhhhhhhhh....eee..hhhhh.............hhhhh.eeee..eeee...........................hhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee...........eee...hhhhhhhhhhhhhhhhhhhhhh......hhhhheeeee..eeee....hhhhh....eeeeee..eeeeeeee.eeeeee......eeeeee.............hhhhhhhhh...ee...hhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3srb B 217 SNAIAVGSERSADGKGMLLANPHFPWNGAMRFYQMHLTIPGRLDVMGASLPGLPVVNIGFSRHLAWTHTVDTSSHFTLYRLALDPKDPRRYLVDGRSLPLEEKSVAIEVRGADGKLSRVEHKVYQSIYGPLVVWPGKLDWNRSEAYALRDANLENTRVLQQWYSINQASDVADLRRRVEALQGIPWVNTLAADEQGNALYMNQSVVPYLKPELIPACAIPQLVAEGLPALQGQDSRCAWSRDPAAAQAGITPAAQLPVLLRRDFVQNSNDSAWLTNPASPLQGFSPLVSQEKPIGPRARYALSRLQGKQPLEAKTLEEMVTANHVFSADQVLPDLLRLCRDNQGEKSLARACAALAQWDRGANLDSGSGFVYFQRFMQRFAELDGAWKEPFDAQRPLDTPQGIALDRPQVATQVRQALADAAAEVEKSGIPDGARWGDLQVSTRGQERIAIPGGDGHFGVYNAIQSVRKGDHLEVVGGTSYIQLVTFPEEGPKARGLLAFSQSSDPRSPHYRDQTELFSRQQWQTLPFSDRQIDADPQLQRLSIRE 762
                                   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 3SRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2wyb 2wyc 2wyd 2wye 3l91 3l94 3sra 3src