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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
 
Authors :  H. M. Holden, M. M. Benning, F. M. Raushel, H. Shim
Date :  26 Jan 01  (Deposition) - 04 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pte, Hydrolase, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. M. Benning, H. Shim, F. M. Raushel, H. M. Holden
High Resolution X-Ray Structures Of Different Metal-Substituted Forms Of Phosphotriesterase From Pseudomonas Diminuta.
Biochemistry V. 40 2712 2001
PubMed-ID: 11258882  |  Reference-DOI: 10.1021/BI002661E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOTRIESTERASE
    ChainsA, B
    EC Number3.1.8.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificBREVUNDIMONAS DIMINUTA
    Organism Taxid293
    SynonymPARATHION HYDROLASE, PTE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric/Biological Unit (5, 30)
No.NameCountTypeFull Name
1EDO20Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID
3NA2Ligand/IonSODIUM ION
4PEL2Ligand/Ion2-PHENYL-ETHANOL
5ZN4Ligand/IonZINC ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:301 , FMT A:369 , ZN A:402 , EDO A:408 , HOH A:876BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:201 , HIS A:230 , FMT A:369 , ZN A:401 , HOH A:876 , HOH A:897BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREHIS B:55 , HIS B:57 , ASP B:301 , FMT B:369 , ZN B:402 , EDO B:407 , HOH B:831BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREHIS B:201 , HIS B:230 , FMT B:369 , ZN B:401 , HOH B:831 , HOH B:919BINDING SITE FOR RESIDUE ZN B 402
05AC5SOFTWAREASN A:38 , ILE A:154 , HOH A:436 , HOH A:815 , HOH A:963BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWAREASN B:38 , ILE B:154 , HOH B:635 , HOH B:812 , HOH B:873BINDING SITE FOR RESIDUE NA B 406
07AC7SOFTWAREHIS B:57 , ILE B:106 , TRP B:131 , FMT B:369 , ZN B:401 , EDO B:422 , EDO B:423 , HOH B:919BINDING SITE FOR RESIDUE EDO B 407
08AC8SOFTWAREHIS A:57 , ILE A:106 , TRP A:131 , PHE A:306 , FMT A:369 , ZN A:401 , EDO A:425 , EDO A:426 , HOH A:897BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWAREARG A:91 , THR B:147 , HOH B:722 , HOH B:813 , HOH B:1060BINDING SITE FOR RESIDUE EDO B 409
10BC1SOFTWARELEU A:182 , HOH A:541 , HOH A:838 , HOH A:853 , HOH A:1177BINDING SITE FOR RESIDUE EDO A 410
11BC2SOFTWAREGLU A:115 , HOH A:498 , HOH A:890BINDING SITE FOR RESIDUE EDO A 411
12BC3SOFTWARETHR A:147 , ARG A:189 , HOH A:563 , HOH A:808 , HOH A:906 , ARG B:91BINDING SITE FOR RESIDUE EDO A 412
13BC4SOFTWAREARG B:76 , GLU B:115BINDING SITE FOR RESIDUE EDO B 413
14BC5SOFTWAREGLY B:305 , PHE B:306 , MET B:314 , HOH B:779BINDING SITE FOR RESIDUE EDO B 414
15BC6SOFTWAREPRO B:256 , TRP B:277 , VAL B:320 , PHE B:327 , HOH B:825 , HOH B:1178BINDING SITE FOR RESIDUE EDO B 415
16BC7SOFTWAREASP A:133 , PRO A:134 , PRO A:135 , HOH A:469 , HOH A:472 , HOH A:537 , ASP B:133 , PRO B:134 , PRO B:135BINDING SITE FOR RESIDUE EDO A 416
17BC8SOFTWAREVAL A:351 , HOH A:450 , HOH A:993 , HOH A:1119BINDING SITE FOR RESIDUE EDO A 417
18BC9SOFTWAREALA A:266 , SER A:269 , ALA A:270BINDING SITE FOR RESIDUE EDO A 418
19CC1SOFTWARESER A:276 , THR A:279 , HOH A:594BINDING SITE FOR RESIDUE EDO A 419
20CC2SOFTWAREPRO A:256 , TRP A:277 , VAL A:320 , PHE A:327 , HOH A:877BINDING SITE FOR RESIDUE EDO A 420
21CC3SOFTWARETRP B:131 , PHE B:132 , PRO B:134 , THR B:177 , GLN B:180 , HOH B:700 , HOH B:702BINDING SITE FOR RESIDUE EDO B 421
22CC4SOFTWARESER B:308 , TYR B:309 , EDO B:407 , HOH B:920 , HOH B:1191BINDING SITE FOR RESIDUE EDO B 422
23CC5SOFTWAREHIS B:257 , ASP B:301 , EDO B:407 , HOH B:831 , HOH B:1124BINDING SITE FOR RESIDUE EDO B 423
24CC6SOFTWAREHOH A:1120 , SER B:47 , GLU B:48 , GLY B:50 , ARG B:96BINDING SITE FOR RESIDUE EDO B 424
25CC7SOFTWAREHIS A:254 , HIS A:257 , ASP A:301 , EDO A:408BINDING SITE FOR RESIDUE EDO A 425
26CC8SOFTWARESER A:308 , TYR A:309 , EDO A:408 , HOH A:1190BINDING SITE FOR RESIDUE EDO A 426
27CC9SOFTWARELYS B:77 , MET B:293 , THR B:345 , GLY B:348 , ASN B:353BINDING SITE FOR RESIDUE PEL B 427
28DC1SOFTWARELYS A:77 , MET A:293 , LYS A:294 , THR A:345 , GLY A:348 , ILE A:349 , ASN A:353BINDING SITE FOR RESIDUE PEL A 428
29DC2SOFTWAREHIS A:55 , HIS A:57 , ILE A:106 , LYS A:169 , HIS A:201 , HIS A:230 , ZN A:401 , ZN A:402 , EDO A:408 , HOH A:876BINDING SITE FOR RESIDUE FMT A 369
30DC3SOFTWAREHIS B:55 , HIS B:57 , LYS B:169 , HIS B:201 , HIS B:230 , ZN B:401 , ZN B:402 , EDO B:407 , HOH B:831BINDING SITE FOR RESIDUE FMT B 369

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HZY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOTRIESTERASE_2PS51347 Phosphotriesterase family profile.OPD_BREDI35-363
 
  2A:35-363
B:35-363
2PHOSPHOTRIESTERASE_1PS01322 Phosphotriesterase family signature 1.OPD_BREDI50-58
 
  2A:50-58
B:50-58

(-) Exons   (0, 0)

(no "Exon" information available for 1HZY)

(-) 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:331
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:331
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 
            OPD_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
               SCOP domains d1hzya_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1hzyA00 A:35-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: A:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hzy A  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 

Chain B from PDB  Type:PROTEIN  Length:331
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:331
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 
            OPD_BREDI    35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
               SCOP domains d1hzyb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1hzyB00 B:35-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eee.....hhhhhh.hhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHOTRIESTERASE_2  PDB: B:35-363 UniProt: 35-363                                                                                                                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) ---------------PHOSPHOTR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hzy B  35 DRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRAS 365
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OPD_BREDI | P0A434)
molecular function
    GO:0004063    aryldialkylphosphatase activity    Catalysis of the reaction: aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol.
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OPD_BREDI | P0A4341dpm 1eyw 1ez2 1i0b 1i0d 1jgm 1psc 1pta 1qw7 2o4m 2o4q 2ob3 2oql 3cak 3cs2 3e3h 3upm 3ur2 3ur5 3ura 3urb 3urn 3urq 4e3t 4gy0 4gy1 4zst 4zsu

(-) Related Entries Specified in the PDB File

1i03 1I03 REPRESENTS THE CADMIUM-CONTAINING ENZYME