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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE MANGANESE-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, Hydrolase, Manganese (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, 36)

Asymmetric/Biological Unit (5, 36)
No.NameCountTypeFull Name
1EDO26Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID
3MN4Ligand/IonMANGANESE (II) ION
4NA2Ligand/IonSODIUM ION
5PEL2Ligand/Ion2-PHENYL-ETHANOL

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:301 , FMT A:369 , MN A:402 , EDO A:408 , HOH A:1010BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREHIS A:201 , HIS A:230 , FMT A:369 , MN A:401 , HOH A:853 , HOH A:1010 , HOH A:1012BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWAREHIS B:55 , HIS B:57 , ASP B:301 , FMT B:369 , MN B:402 , EDO B:407 , HOH B:1009BINDING SITE FOR RESIDUE MN B 401
04AC4SOFTWAREHIS B:201 , HIS B:230 , FMT B:369 , MN B:401 , HOH B:1009 , HOH B:1011 , HOH B:1015BINDING SITE FOR RESIDUE MN B 402
05AC5SOFTWAREASN A:38 , ILE A:154 , GLN A:155 , ARG A:164 , HOH A:787 , HOH A:1014BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWAREASN B:38 , ILE B:154 , GLN B:155 , ARG B:164 , HOH B:785 , HOH B:806 , HOH B:1018BINDING SITE FOR RESIDUE NA B 406
07AC7SOFTWAREHIS B:57 , ILE B:106 , TRP B:131 , FMT B:369 , MN B:401 , HOH B:530 , HOH B:1011 , HOH B:1127BINDING SITE FOR RESIDUE EDO B 407
08AC8SOFTWAREHIS A:57 , TRP A:131 , PHE A:306 , FMT A:369 , MN A:401 , HOH A:854 , HOH A:995 , HOH A:1010 , HOH A:1012BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWAREARG A:91 , THR B:147 , HOH B:710 , HOH B:786BINDING SITE FOR RESIDUE EDO B 409
10BC1SOFTWARELEU A:182 , HOH A:558BINDING SITE FOR RESIDUE EDO A 410
11BC2SOFTWAREVAL A:84 , GLU A:115 , HOH A:796BINDING SITE FOR RESIDUE EDO A 411
12BC3SOFTWAREEDO A:413 , HOH A:559 , HOH A:783 , HOH A:1016 , ARG B:91BINDING SITE FOR RESIDUE EDO A 412
13BC4SOFTWAREEDO A:412 , HOH A:1016 , ARG B:91 , ASP B:121 , HOH B:676BINDING SITE FOR RESIDUE EDO A 413
14BC5SOFTWARELYS B:77 , GLU B:115 , HOH B:1059BINDING SITE FOR RESIDUE EDO B 414
15BC6SOFTWAREPRO B:256 , TRP B:277 , VAL B:320 , PHE B:327BINDING SITE FOR RESIDUE EDO B 415
16BC7SOFTWAREASP A:133 , PRO A:134 , PRO A:135 , ASP B:133 , PRO B:134 , PRO B:135 , HOH B:472 , HOH B:475 , HOH B:836BINDING SITE FOR RESIDUE EDO B 416
17BC8SOFTWARESER A:47 , GLU A:48 , GLY A:50 , ARG A:96BINDING SITE FOR RESIDUE EDO A 417
18BC9SOFTWARESER B:47 , GLU B:48 , GLY B:50 , ARG B:96 , HIS B:123 , HOH B:636 , HOH B:989BINDING SITE FOR RESIDUE EDO B 418
19CC1SOFTWAREARG A:41 , GLY A:42 , PRO A:43 , EDO B:423BINDING SITE FOR RESIDUE EDO A 419
20CC2SOFTWAREPHE A:72 , PHE A:73 , GLY A:305 , PHE A:306 , MET A:314 , HOH A:489BINDING SITE FOR RESIDUE EDO A 420
21CC3SOFTWAREPRO B:70 , GLU B:71 , SER B:75 , ARG B:76 , HOH B:550 , HOH B:655 , HOH B:939BINDING SITE FOR RESIDUE EDO B 421
22CC4SOFTWAREASN B:265 , SER B:267 , VAL B:310 , THR B:311 , ASN B:312 , ILE B:313 , VAL B:316 , HOH B:930BINDING SITE FOR RESIDUE EDO B 422
23CC5SOFTWAREGLY A:42 , PRO A:43 , EDO A:419 , HOH A:440 , HOH A:883 , HOH A:923 , PRO B:334 , GLU B:338BINDING SITE FOR RESIDUE EDO B 423
24CC6SOFTWAREARG A:337 , GLN A:343 , HOH A:457 , TYR B:156 , HOH B:698BINDING SITE FOR RESIDUE EDO A 424
25CC7SOFTWARETHR B:352 , ALA B:355 , HOH B:635BINDING SITE FOR RESIDUE EDO B 425
26CC8SOFTWAREPHE A:104 , ARG A:108 , GLU A:159 , HOH A:476 , GLY B:64 , ARG B:67 , ALA B:68BINDING SITE FOR RESIDUE EDO B 426
27CC9SOFTWAREGLN A:295 , ARG A:356 , HOH A:984BINDING SITE FOR RESIDUE EDO A 427
28DC1SOFTWARELYS B:285 , LYS B:339 , GLY B:340 , HOH B:758BINDING SITE FOR RESIDUE EDO B 428
29DC2SOFTWAREGLY B:74 , ALA B:78 , HOH B:810BINDING SITE FOR RESIDUE EDO B 429
30DC3SOFTWAREGLY A:74 , ALA A:78 , HOH A:934BINDING SITE FOR RESIDUE EDO A 430
31DC4SOFTWAREARG B:118 , HOH B:906BINDING SITE FOR RESIDUE EDO B 431
32DC5SOFTWAREGLU A:210 , ALA A:242 , ARG A:246 , HOH A:576BINDING SITE FOR RESIDUE EDO A 432
33DC6SOFTWARELYS B:77 , MET B:293 , GLY B:348 , ASN B:353 , ARG B:356BINDING SITE FOR RESIDUE PEL B 433
34DC7SOFTWARELYS 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 434
35DC8SOFTWAREHIS A:55 , HIS A:57 , ILE A:106 , TRP A:131 , LYS A:169 , HIS A:201 , HIS A:230 , MN A:401 , MN A:402 , EDO A:408 , HOH A:1010 , HOH A:1012BINDING SITE FOR RESIDUE FMT A 369
36DC9SOFTWAREHIS B:55 , HIS B:57 , LYS B:169 , HIS B:201 , HIS B:230 , MN B:401 , MN B:402 , EDO B:407 , HOH B:1009BINDING SITE FOR RESIDUE FMT B 369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I0B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I0B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I0B)

(-) 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 1I0B)

(-) 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 d1i0ba_ A: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1i0bA00 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.....hhhhhhhhhhhh...hhh.eee.hhhhh.hhhhhhhhhhhh.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
                 1i0b 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 d1i0bb_ B: Phosphotriesterase (parathion hydrolase, PTE)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1i0bB00 B:34-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.hhhh.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
                 1i0b 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)
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  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 1I0B)

(-) 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 1hzy 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

1hzy 1HZY REPRESENTS THE ZINC-CONTAINING ENZYME
1i03 1I03 REPRESENTS THE CADMIUM-CONTAINING ENZYME
1i0d 1I0D REPRESENTS THE ZINC AND CADMIUM-CONTAINING ENZYME