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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF METHYL PARATHION HYDROLASE FROM PSEUDOMONAS SP WBC-3
 
Authors :  Y. Dong, L. Sun, M. Bartlam, Z. Rao, X. Zhang
Date :  11 May 03  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Zn Containing, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Dong, L. Sun, M. Bartlam, Z. Rao, X. Zhang
Crystal Structure Analysis Of Methyl Parathion Hydrolase From Pseudomonas Sp Wbc-3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYL PARATHION HYDROLASE
    Chains: A, B
    EC Number: 3.1.8.1
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 165468
    Strain: WBC-3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2K4Ligand/IonPOTASSIUM ION
3NA5Ligand/IonSODIUM ION
4ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2K-1Ligand/IonPOTASSIUM ION
3NA-1Ligand/IonSODIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2K-1Ligand/IonPOTASSIUM ION
3NA-1Ligand/IonSODIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:151 , HIS A:152 , ASP A:255 , HIS A:302 , HOH A:608BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:147 , HIS A:149 , HIS A:234 , ASP A:255 , HOH A:608 , HOH A:772BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREASP B:151 , HIS B:152 , ASP B:255 , HIS B:302 , HOH B:666BINDING SITE FOR RESIDUE ZN B 1401
04AC4SOFTWAREHIS B:147 , HIS B:149 , HIS B:234 , ASP B:255 , HOH B:609 , HOH B:666BINDING SITE FOR RESIDUE CD B 1402
05AC5SOFTWAREGLU A:142 , NA A:505 , HOH A:693 , HOH B:694BINDING SITE FOR RESIDUE K A 501
06AC6SOFTWAREASP A:172 , HIS A:232 , HOH A:695BINDING SITE FOR RESIDUE K A 502
07AC7SOFTWAREGLN A:136 , GLU A:138 , HOH A:696BINDING SITE FOR RESIDUE K A 503
08AC8SOFTWAREASP A:221 , ASP B:54BINDING SITE FOR RESIDUE K B 504
09AC9SOFTWAREVAL A:168 , LYS A:214 , K A:501BINDING SITE FOR RESIDUE NA A 505
10BC1SOFTWAREGLU A:244BINDING SITE FOR RESIDUE NA A 506
11BC2SOFTWAREGLN B:136 , GLU B:138BINDING SITE FOR RESIDUE NA B 507
12BC3SOFTWARELYS B:174 , HIS B:232BINDING SITE FOR RESIDUE NA B 508
13BC4SOFTWAREASP B:221 , LYS B:227 , ASP B:290BINDING SITE FOR RESIDUE NA B 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P9E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:305 -Pro A:306
2Ala B:91 -Pro B:92
3Phe B:305 -Pro B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P9E)

(-) Exons   (0, 0)

(no "Exon" information available for 1P9E)

(-) 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:294
 aligned with Q841S6_PSEWB | Q841S6 from UniProtKB/TrEMBL  Length:331

    Alignment length:294
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
         Q841S6_PSEWB    36 AAPQVRTSAPGYYRMLLGDFEITALSDGTVALPVDKRLNQPAPKTQSALAKSFQKAPLETSVTGYLVNTGSKLVLVDTGAAGLFGPTLGRLAANLKAAGYQPEQVDEIYITHMHPDHVGGLMVGEQLAFPNAVVRADQKEADFWLSQTNLDKAPDDESKGFFKGAMASLNPYVKAGKFKPFSGNTDLVPGIKALASHGHTPGHTTYVVESQGQKLALLGDLILVAAVQFDDPSVTTQLDSDSKSVAVERKKAFADAAKGGYLIAASHLSFPGIGHIRAEGKGYRFVPVNYSVVN 329
               SCOP domains d1p9ea_ A: Methyl parathion hydrolase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1p9eA00 A:36-329 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeeeeeeeeehhhhhh..hhhhhhhhhhhh.....eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhh..ee..ee.....eee.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.........ee....eeeee........eeeeeee..eeeee......hhhhhh...........hhhhhhhhhhhhhhhhhhhh.eee........eeeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p9e A  36 AAPQVRTSAPGYYRMLLGDFEITALSDGTVALPVDKRLNQPAPKTQSALAKSFQKAPLETSVTGYLVNTGSKLVLVDTGAAGLFGPTLGRLAANLKAAGYQPEQVDEIYITHMHPDHVGGLMVGEQLAFPNAVVRADQKEADFWLSQTNLDKAPDDESKGFFKGAMASLNPYVKAGKFKPFSGNTDLVPGIKALASHGHTPGHTTYVVESQGQKLALLGDLILVAAVQFDDPSVTTQLDSDSKSVAVERKKAFADAAKGGYLIAASHLSFPGIGHIRAEGKGYRFVPVNYSVVN 329
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with Q841S6_PSEWB | Q841S6 from UniProtKB/TrEMBL  Length:331

    Alignment length:294
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
         Q841S6_PSEWB    36 AAPQVRTSAPGYYRMLLGDFEITALSDGTVALPVDKRLNQPAPKTQSALAKSFQKAPLETSVTGYLVNTGSKLVLVDTGAAGLFGPTLGRLAANLKAAGYQPEQVDEIYITHMHPDHVGGLMVGEQLAFPNAVVRADQKEADFWLSQTNLDKAPDDESKGFFKGAMASLNPYVKAGKFKPFSGNTDLVPGIKALASHGHTPGHTTYVVESQGQKLALLGDLILVAAVQFDDPSVTTQLDSDSKSVAVERKKAFADAAKGGYLIAASHLSFPGIGHIRAEGKGYRFVPVNYSVVN 329
               SCOP domains d1p9eb_ B: Methyl parathion hydrolase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1p9eB00 B:36-329 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeeeeeeeeehhhhhh..hhhhhhhhhhhh.....eeeeeeeeeee....eeee.............hhhhhhhhh..hhhhh.eee....hhhhhh..ee..ee.....eee.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........ee....eeeee........eeeeeee..eeeee......hhhhhh...........hhhhhhhhhhhhhhhhhhhh.eee........eeeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p9e B  36 AAPQVRTSAPGYYRMLLGDFEITALSDGTVALPVDKRLNQPAPKTQSALAKSFQKAPLETSVTGYLVNTGSKLVLVDTGAAGLFGPTLGRLAANLKAAGYQPEQVDEIYITHMHPDHVGGLMVGEQLAFPNAVVRADQKEADFWLSQTNLDKAPDDESKGFFKGAMASLNPYVKAGKFKPFSGNTDLVPGIKALASHGHTPGHTTYVVESQGQKLALLGDLILVAAVQFDDPSVTTQLDSDSKSVAVERKKAFADAAKGGYLIAASHLSFPGIGHIRAEGKGYRFVPVNYSVVN 329
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P9E)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q841S6_PSEWB | Q841S6)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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