Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF PSEUDOMONAS AERUGIONSA PVDQ BOUND TO OCTANOATE
 
Authors :  E. J. Drake, A. M. Gulick
Date :  04 Jan 10  (Deposition) - 19 Jan 11  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pvdq, Pyoverdine, Acylase, Ntn Hydrolase, Quorum Sensing, Zymogen, Hydrolase (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 SUBUNIT ALPHA
    Chains: A
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Gene: PA2385, PVDQ, QSC112
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PA01
    Synonym: ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA
 
Molecule 2 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
    Chains: B
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Gene: PA2385, PVDQ, QSC112
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PA01
    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, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2OCA1Ligand/IonOCTANOIC ACID (CAPRYLIC ACID)

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:70 , TRP A:153 , ARG A:155 , HOH A:259BINDING SITE FOR RESIDUE EDO A 901
02AC2SOFTWAREARG A:77 , GLU A:79 , HOH A:218 , HOH A:227BINDING SITE FOR RESIDUE EDO A 902
03AC3SOFTWARELEU A:97 , VAL A:183 , HOH A:206 , HOH A:943 , PRO B:256 , GLY B:257 , HIS B:337 , HOH B:890BINDING SITE FOR RESIDUE EDO A 907
04AC4SOFTWAREARG A:36 , ARG A:46 , ALA A:186 , PRO A:187 , HOH A:841 , ARG B:757BINDING SITE FOR RESIDUE EDO A 910
05AC5SOFTWAREGLU A:172 , GLN A:177 , TRP B:402BINDING SITE FOR RESIDUE EDO A 914
06AC6SOFTWARELEU A:169 , HOH B:122 , SER B:217 , PRO B:238 , PHE B:240 , ASN B:273 , ILE B:274 , HIS B:284 , THR B:285 , VAL B:286 , TRP B:378 , VAL B:403 , HOH B:887 , EDO B:915BINDING SITE FOR RESIDUE OCA B 1
07AC7SOFTWAREHOH A:5 , TYR A:40 , GLN B:250 , GLN B:730 , THR B:741 , LEU B:742 , PRO B:743BINDING SITE FOR RESIDUE EDO B 900
08AC8SOFTWARESER A:91 , ARG A:168 , PRO B:241 , ASN B:243 , GLY B:244 , ALA B:245 , MET B:246BINDING SITE FOR RESIDUE EDO B 903
09AC9SOFTWAREHOH B:113 , LEU B:259 , ASP B:260 , ASN B:382BINDING SITE FOR RESIDUE EDO B 904
10BC1SOFTWARESER A:86 , LEU A:97 , HOH A:858 , GLY B:257 , HOH B:890 , EDO B:906BINDING SITE FOR RESIDUE EDO B 905
11BC2SOFTWAREHOH B:113 , GLY B:257 , ARG B:258 , EDO B:905BINDING SITE FOR RESIDUE EDO B 906
12BC3SOFTWAREARG B:278 , GLU B:410 , PHE B:703 , PRO B:704 , GLY B:707 , PRO B:708BINDING SITE FOR RESIDUE EDO B 908
13BC4SOFTWAREHOH B:193 , HOH B:196 , PRO B:704 , GLU B:706 , GLY B:707 , PRO B:708BINDING SITE FOR RESIDUE EDO B 909
14BC5SOFTWAREHOH B:75 , HOH B:77 , THR B:372 , ARG B:373 , ALA B:462 , HOH B:780BINDING SITE FOR RESIDUE EDO B 911
15BC6SOFTWAREHOH B:141 , ARG B:365 , TRP B:455 , ARG B:457 , ALA B:464 , GLY B:465BINDING SITE FOR RESIDUE EDO B 912
16BC7SOFTWAREHOH B:174 , PHE B:596 , ALA B:597 , LEU B:599 , GLY B:601 , ALA B:602 , TRP B:603BINDING SITE FOR RESIDUE EDO B 913
17BC8SOFTWAREOCA B:1 , LEU B:269 , VAL B:271 , ASN B:273 , TRP B:378 , HOH B:891BINDING SITE FOR RESIDUE EDO B 915
18BC9SOFTWAREHOH B:10 , LEU B:308 , GLY B:311 , ASP B:729 , GLU B:732BINDING SITE FOR RESIDUE EDO B 916
19CC1SOFTWAREVAL B:587 , ARG B:591 , SER B:644 , ARG B:684BINDING SITE FOR RESIDUE EDO B 917
20CC2SOFTWAREASP B:581 , ASP B:654BINDING SITE FOR RESIDUE EDO B 918

(-) 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 3L91)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L91)

(-) Exons   (0, 0)

(no "Exon" information available for 3L91)

(-) 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 ...eeeeeeehhheeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l91 A  29 TGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAEK 192
                                    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 (1) Penicil_amidase-3l91B01 B:217-755                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (1)
           Pfam domains (2) Penicil_amidase-3l91B02 B:217-755                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (2)
         Sec.struct. author .eeeee..........eeeee.eee.......eeeeeee...eeeeeee........eee...eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeeeeee.....eeeeeeeeeee..eeee...........eeeeeee.hhhh.hhhhhhhhhhh..hhhhhhhhhhhhh....eeeeeee....eeee........hhhhhhhhhhhhhhh....eee..hhhhh.............hhhhh.eeee..eeee...........................hhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee...........eee...hhhhhhhhhhhhhhhhhhhhhh......hhhhheeeee..eeee....hhhhh....eeeeee..eeeeeeee.eeeeee......eeeeee.............hhhhhhhhhh..ee...hhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l91 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 3L91)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L91)

(-) 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).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr B:615 - Pro B:616   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3l91
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PVDQ_PSEAE | Q9I194
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.1.97
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PVDQ_PSEAE | Q9I194
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3l94