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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE ENZYME PAGL
 
Authors :  L. Rutten, J. Geurtsen, W. Lambert, J. J. Smolenaers, A. M. Bonvin, P. Va Ley, M. R. Egmond, P. Gros, J. Tommassen
Date :  25 Oct 05  (Deposition) - 11 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Outer Membrane, Enzyme, Hydrolase, Lipopolysaccharide, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Rutten, J. Geurtsen, W. Lambert, J. J. Smolenaers, A. M. Bonvin, A. De Haan, P. Van Der Ley, M. R. Egmond, P. Gros, J. Tommassen
Crystal Structure And Catalytic Mechanism Of The Lps 3-O-Deacylase Pagl From Pseudomonas Aeruginosa.
Proc. Natl. Acad. Sci. Usa V. 103 7071 2006
PubMed-ID: 16632613  |  Reference-DOI: 10.1073/PNAS.0509392103

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PAER03002360
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPAGL(PA)(-)
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PET-11A
    Gene: PA4661
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CXE12Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CXE4Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CXE8Ligand/IonPENTAETHYLENE GLYCOL MONODECYL ETHER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:106 , ASP B:106 , CXE B:1200BINDING SITE FOR RESIDUE CA A 195
02AC2SOFTWARETRP B:25 , TRP B:41 , ILE B:83BINDING SITE FOR RESIDUE CXE B 196
03AC3SOFTWAREILE A:108 , ALA A:124 , ALA B:130 , LEU B:132BINDING SITE FOR RESIDUE CXE B 200
04AC4SOFTWARETRP A:25BINDING SITE FOR RESIDUE CXE A 300
05AC5SOFTWAREMET B:15 , VAL B:122 , TYR B:142 , SER B:143BINDING SITE FOR RESIDUE CXE B 400
06AC6SOFTWAREILE A:75 , GLY B:111BINDING SITE FOR RESIDUE CXE B 500
07AC7SOFTWAREMET A:15 , TYR A:142 , HOH A:859BINDING SITE FOR RESIDUE CXE A 600
08AC8SOFTWAREGLY A:111BINDING SITE FOR RESIDUE CXE A 700
09AC9SOFTWARELEU B:19BINDING SITE FOR RESIDUE CXE A 800
10BC1SOFTWAREPHE B:62 , PRO B:64 , ILE B:83BINDING SITE FOR RESIDUE CXE B 900
11BC2SOFTWAREVAL B:85 , LEU B:102 , PHE B:104 , ASN B:129BINDING SITE FOR RESIDUE CXE B 1000
12BC3SOFTWAREALA A:130 , ILE B:83 , ARG B:107 , ILE B:108 , GLU B:140 , TYR B:142 , CXE B:1200BINDING SITE FOR RESIDUE CXE B 1100
13BC4SOFTWAREPHE A:104 , ASP A:106 , SER A:128 , CA A:195 , PHE B:104 , ASP B:106 , HIS B:126 , SER B:128 , CXE B:1100BINDING SITE FOR RESIDUE CXE B 1200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ERV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:134 -Pro A:135
2Gln B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ERV)

(-) Sequences/Alignments

Asymmetric 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:150
 aligned with PAGL_PSEAE | Q9HVD1 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:150
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
           PAGL_PSEAE    24 ADVSAAVGATGQSGMTYRLGLSWDWDKSWWQTSTGRLTGYWDAGYTYWEGGDEGAGKHSLSFAPVFVYEFAGDSIKPFIEAGIGVAAFSGTRVGDQNLGSSLNFEDRIGAGLKFANGQSVGVRAIHYSNAGLKQPNDGIESYSLFYKIPI 173
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ervA00 A:1-150  [code=2.40.160.20, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeeeeee....eeee..eeeeeeeeeeeeee........eeeeeeeeeeeeee....eeeeeeeeeeeeee...ee..ee....eeeeeeeeeeeee....eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2erv A   1 ADVSAAVGATGQSGMTYRLGLSWDWDKSWWQTSTGRLTGYWDAGYTYWEGGDEGAGKHSLSFAPVFVYEFAGDSIKPFIEAGIGVAAFSGTRVGDQNLGSSLNFEDRIGAGLKFANGQSVGVRAIHYSNAGLKQPNDGIESYSLFYKIPI 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with PAGL_PSEAE | Q9HVD1 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:150
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
           PAGL_PSEAE    24 ADVSAAVGATGQSGMTYRLGLSWDWDKSWWQTSTGRLTGYWDAGYTYWEGGDEGAGKHSLSFAPVFVYEFAGDSIKPFIEAGIGVAAFSGTRVGDQNLGSSLNFEDRIGAGLKFANGQSVGVRAIHYSNAGLKQPNDGIESYSLFYKIPI 173
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ervB00 B:1-150  [code=2.40.160.20, no name define    d]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....eeeeeeeeee....eeee..eeeeeeeeeeeeee..----..eeeeeeeeeeeeee....eeeeeeeeeeeeee...ee..ee....eeeeeeeeeeeee....eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2erv B   1 ADVSAAVGATGQSGMTYRLGLSWDWDKSWWQTSTGRLTGYWDAGYTYWEG----AGKHSLSFAPVFVYEFAGDSIKPFIEAGIGVAAFSGTRVGDQNLGSSLNFEDRIGAGLKFANGQSVGVRAIHYSNAGLKQPNDGIESYSLFYKIPI 150
                                    10        20        30        40        50    |   60        70        80        90       100       110       120       130       140       150
                                                                            50   55
   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 2ERV)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ERV)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAGL_PSEAE | Q9HVD1)
molecular function
    GO:0050528    acyloxyacyl hydrolase activity    Catalysis of the reaction: 3-(acyloxy)acyl group of bacterial toxin = 3-hydroxyacyl group of bacterial toxin + a fatty acid.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0046493    lipid A metabolic process    The chemical reactions and pathways involving lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0008653    lipopolysaccharide metabolic process    The chemical reactions and pathways involving lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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