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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE ZINC/CADMIUM-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
 
Authors :  H. M. Holden, M. M. Benning, F. M. Raushel, H. Shim
Date :  29 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, Zinc, Cadmium, Mixed Metals, Hydrolase (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
    Chains: A, B
    EC Number: 3.1.8.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BREVUNDIMONAS DIMINUTA
    Organism Taxid: 293
    Synonym: PARATHION HYDROLASE, PTE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric/Biological Unit (6, 25)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3FMT2Ligand/IonFORMIC ACID
4NA2Ligand/IonSODIUM ION
5PEL2Ligand/Ion2-PHENYL-ETHANOL
6ZN2Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:301 , FMT A:369 , CD A:402 , EDO A:406 , HOH A:1054BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:201 , HIS A:230 , FMT A:369 , ZN A:401 , HOH A:876 , HOH A:1054 , HOH A:1056BINDING SITE FOR RESIDUE CD A 402
03AC3SOFTWAREHIS B:55 , HIS B:57 , ASP B:301 , FMT B:369 , CD B:402 , EDO B:405 , HOH B:1053BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREHIS B:201 , HIS B:230 , FMT B:369 , ZN B:401 , HOH B:1053 , HOH B:1055 , HOH B:1059BINDING SITE FOR RESIDUE CD B 402
05AC5SOFTWAREASN A:38 , ILE A:154 , HOH A:796 , HOH A:1058 , HOH A:1063BINDING SITE FOR RESIDUE NA A 403
06AC6SOFTWAREASN B:38 , ILE B:154 , HOH B:794 , HOH B:818 , HOH B:1062BINDING SITE FOR RESIDUE NA B 404
07AC7SOFTWAREHIS B:57 , TRP B:131 , ASP B:301 , FMT B:369 , ZN B:401 , EDO B:420 , HOH B:524 , HOH B:1053 , HOH B:1055BINDING SITE FOR RESIDUE EDO B 405
08AC8SOFTWAREHIS A:57 , ILE A:106 , TRP A:131 , FMT A:369 , ZN A:401 , EDO A:421 , HOH A:1054 , HOH A:1056BINDING SITE FOR RESIDUE EDO A 406
09AC9SOFTWAREARG A:91 , THR B:147 , HOH B:715 , HOH B:795 , HOH B:1129BINDING SITE FOR RESIDUE EDO B 407
10BC1SOFTWAREHOH A:802 , HOH A:1057 , HOH A:1066 , HOH A:1087BINDING SITE FOR RESIDUE EDO A 408
11BC2SOFTWAREGLU A:81 , VAL A:84 , GLU A:115 , ALA A:119 , HOH A:488 , HOH A:823BINDING SITE FOR RESIDUE EDO A 409
12BC3SOFTWARETHR A:147 , ARG A:189 , EDO A:411 , HOH A:555 , HOH A:792 , HOH A:1060 , ARG B:91BINDING SITE FOR RESIDUE EDO A 410
13BC4SOFTWAREEDO A:410 , ARG B:91 , ASP B:121BINDING SITE FOR RESIDUE EDO A 411
14BC5SOFTWARELYS B:77 , ALA B:80 , GLU B:115 , GLU B:344 , HOH B:1116BINDING SITE FOR RESIDUE EDO B 412
15BC6SOFTWAREPRO B:256 , TRP B:277 , VAL B:320 , PHE B:327 , HOH B:798BINDING SITE FOR RESIDUE EDO B 413
16BC7SOFTWARELYS B:77 , MET B:293 , LYS B:294 , GLY B:348 , ASN B:353BINDING SITE FOR RESIDUE PEL B 414
17BC8SOFTWARELYS A:77 , MET A:293 , THR A:345 , GLY A:348 , ILE A:349 , ASN A:353 , HOH A:890BINDING SITE FOR RESIDUE PEL A 415
18BC9SOFTWAREASP A:133 , PRO A:134 , PRO A:135 , HOH A:459 , HOH A:460 , HOH A:462 , ASP B:133 , PRO B:134 , PRO B:135 , HOH B:521BINDING SITE FOR RESIDUE EDO A 416
19CC1SOFTWARESER A:47 , GLU A:48 , ARG A:96BINDING SITE FOR RESIDUE EDO A 417
20CC2SOFTWARESER B:47 , GLU B:48 , GLY B:50 , ARG B:96 , HIS B:123 , HOH B:639 , HOH B:1030BINDING SITE FOR RESIDUE EDO B 418
21CC3SOFTWAREARG A:41 , GLY A:42 , PRO A:43 , GLU B:338 , HOH B:803BINDING SITE FOR RESIDUE EDO A 419
22CC4SOFTWAREHIS B:257 , ASP B:301 , LEU B:303 , EDO B:405 , HOH B:1053BINDING SITE FOR RESIDUE EDO B 420
23CC5SOFTWAREPHE A:306 , SER A:308 , TYR A:309 , EDO A:406BINDING SITE FOR RESIDUE EDO A 421
24CC6SOFTWAREHIS A:55 , HIS A:57 , LYS A:169 , HIS A:201 , HIS A:230 , ZN A:401 , CD A:402 , EDO A:406 , HOH A:1054BINDING SITE FOR RESIDUE FMT A 369
25CC7SOFTWAREHIS B:55 , HIS B:57 , LYS B:169 , HIS B:201 , HIS B:230 , ZN B:401 , CD B:402 , EDO B:405 , HOH B:1053BINDING SITE FOR RESIDUE FMT B 369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I0D)

(-) 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 1I0D)

(-) 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 d1i0da_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1i0dA00 A:35-365 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhhhh.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
                 1i0d 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
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
            OPD_BREDI    34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
               SCOP domains d1i0db_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1i0dB00 B:34-364 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
                 1i0d B  34 GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA 364
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I0D)

(-) 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 | P0A434: 1dpm 1eyw 1ez2 1hzy 1i0b 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

1hzy 1HZY REPRESENTS THE ZINC-CONTAINING ENZYME
1i03 1I03 REPRESENTS THE CADMIUM-CONTAINING ENZYME
1i0b 1I0B REPRESENTS THE MANGANESE-CONTAINING ENZYME