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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA PVDQ IN COMPLEX WITH A TRANSITION STATE ANALOGUE
 
Authors :  R. Wu, K. Clevenger, J. Er, W. L. Fast, D. Liu
Date :  02 Aug 13  (Deposition) - 28 Aug 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Transition State Analogue, Heterodimer, Acylase, Boronic Acid, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Clevenger, R. Wu, J. A. Er, D. Liu, W. Fast
Rational Design Of A Transition State Analogue With Picomolar Affinity For Pseudomonas Aeruginosa Pvdq, A Siderophore Biosynthetic Enzyme.
Acs Chem. Biol. V. 8 2192 2013
PubMed-ID: 23883096  |  Reference-DOI: 10.1021/CB400345H

(-) Compounds

Molecule 1 - ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
    Chains: C
    EC Number: 3.5.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 217-762
    Gene: PA2385, PVDQ, QSC112
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: ACYL-HSL ACYLASE PVDQ SUBUNIT BETA, PVDQ NTN-HYDROLASE ACYLASE BETA SUBUNIT
 
Molecule 2 - 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
    Fragment: UNP RESIDUES 28-192
    Gene: PVDQ, QSC112, PA2385
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA, PVDQ NTN-HYDROLASE ACYLASE ALPHA SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1B0S1Ligand/IonTRIDECYLBORONIC ACID
2GOL20Ligand/IonGLYCEROL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER C:217 , HIS C:239 , PHE C:240 , THR C:285 , VAL C:286 , VAL C:374 , TRP C:378 , ASN C:485 , HOH C:1011BINDING SITE FOR RESIDUE B0S C 801
02AC2SOFTWARELEU C:259 , ASP C:260 , ASN C:382 , HOH C:942 , HOH C:943BINDING SITE FOR RESIDUE GOL C 802
03AC3SOFTWAREPRO A:98 , ILE A:101 , PRO C:256 , GLY C:257 , HIS C:337 , HOH C:1095 , HOH C:1256BINDING SITE FOR RESIDUE GOL C 803
04AC4SOFTWAREGOL A:205 , HOH A:427 , TYR C:344 , GLY C:345 , PRO C:346 , LEU C:364 , ARG C:365 , ASP C:366 , LEU C:369 , HOH C:1002 , HOH C:1149BINDING SITE FOR RESIDUE GOL C 804
05AC5SOFTWAREARG C:365 , ALA C:454 , TRP C:455 , ARG C:457 , ALA C:464 , GLY C:465BINDING SITE FOR RESIDUE GOL C 805
06AC6SOFTWAREGLU A:72 , SER A:91 , ALA A:92 , ARG A:168 , PRO C:241 , ASN C:243 , GLY C:244 , ALA C:245 , MET C:246BINDING SITE FOR RESIDUE GOL C 806
07AC7SOFTWARETHR C:372 , ARG C:373 , ALA C:462 , GLN C:463 , HOH C:976 , HOH C:992 , HOH C:1013 , HOH C:1039 , HOH C:1136BINDING SITE FOR RESIDUE GOL C 807
08AC8SOFTWAREPHE C:596 , ALA C:597 , GLU C:598 , LEU C:599 , GLY C:601 , ALA C:602 , TRP C:603 , HOH C:1015BINDING SITE FOR RESIDUE GOL C 808
09AC9SOFTWAREILE C:255 , PRO C:256 , GLY C:257 , ARG C:258 , LEU C:259 , ASP C:260 , HOH C:1118 , HOH C:1229BINDING SITE FOR RESIDUE GOL C 809
10BC1SOFTWAREGLN C:498 , GLY C:499BINDING SITE FOR RESIDUE GOL C 810
11BC2SOFTWAREASN C:485 , ASP C:486 , GLY C:511 , HOH C:1093BINDING SITE FOR RESIDUE GOL C 811
12BC3SOFTWARELEU C:580 , ASP C:581 , ARG C:651 , GLY C:653 , ASP C:654 , HOH C:1181BINDING SITE FOR RESIDUE GOL C 812
13BC4SOFTWAREPRO C:459 , ALA C:461 , HOH C:1123 , HOH C:1131BINDING SITE FOR RESIDUE GOL C 813
14BC5SOFTWAREARG C:591 , GLU C:640 , ILE C:646 , ARG C:684BINDING SITE FOR RESIDUE GOL C 814
15BC6SOFTWAREGLN A:177 , GLY C:442 , LEU C:443 , PRO C:444 , HOH C:1059BINDING SITE FOR RESIDUE GOL C 815
16BC7SOFTWAREGLU A:172 , GLY A:173 , GLN A:177 , TRP C:402BINDING SITE FOR RESIDUE GOL A 201
17BC8SOFTWARELYS A:48 , GLU A:93 , LEU A:94 , ASP A:95 , ASP A:180BINDING SITE FOR RESIDUE GOL A 202
18BC9SOFTWAREGLN A:113 , TRP A:116 , THR A:159 , ASP A:160 , HOH A:321 , LYS C:643BINDING SITE FOR RESIDUE GOL A 203
19CC1SOFTWAREPHE A:137 , ALA A:141 , ASP A:142 , GLY A:143 , LYS A:144 , THR A:145 , THR A:146 , HOH A:405BINDING SITE FOR RESIDUE GOL A 204
20CC2SOFTWARETRP A:105 , LEU A:106 , ARG A:167 , HOH A:427 , GOL C:804BINDING SITE FOR RESIDUE GOL A 205
21CC3SOFTWAREALA A:70 , VAL A:74 , ARG A:77 , GLU A:79 , TYR A:83 , TRP A:153 , ARG A:155 , HOH A:344 , HOH A:354 , HOH A:411BINDING 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  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr C:615 -Pro C:616
2Thr A:29 -Gly A:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M1J)

(-) Exons   (0, 0)

(no "Exon" information available for 4M1J)

(-) 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
                 4m1j 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........eeee..eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeeeeee.....eeeeeeeeeee..eeee...........eeeeeee.hhhh.hhhhhhhhhhh..hhhhhhhhhhhhh....eeeeeee....eeee........hhhhhhhhhhhhhhh....eee..hhhhh.............hhhhh.eeee..eeee...........................hhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....eee...........eee...hhhhhhhhhhhhhhhhhhhhh.......hhhhheeeee..eeee....hhhhh....eeeeee..eeeeeeee.eeeeee......eeeeee.............hhhhhhhhh...ee...hhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m1j 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 4M1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M1J)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

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