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(-) Description

Title :  ROUND 18 ARYLESTERASE VARIANT OF PHOSPHOTRIESTERASE WITH BOUND TRANSITION STATE ANALOG
 
Authors :  N. Tokuriki, C. J. Jackson, D. S. Tawfik
Date :  10 Mar 12  (Deposition) - 23 Jan 13  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphotriesterase, Alpha/Beta Hydrolase, Arylesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tokuriki, C. J. Jackson, L. Afriat-Jurnou, K. T. Wyganowski, R. Tang, D. S. Tawfik
Diminishing Returns And Tradeoffs Constrain The Laboratory Optimization Of An Enzyme
Nat Commun V. 3 1257 2012
PubMed-ID: 23212386  |  Reference-DOI: 10.1038/NCOMMS2246

(-) 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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1HLN1Ligand/IonHEXYL(NAPHTHALEN-2-YLOXY)PHOSPHINIC ACID
2ZN6Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:57 , ASP A:301 , ZN A:403 , HOH A:704 , HOH A:706BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:201 , HIS A:230 , ZN A:403 , HOH A:704 , HOH A:706 , HOH A:728BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREHIS A:55 , HIS A:230 , ASP A:301 , ZN A:401 , ZN A:402 , HOH A:704 , HOH A:706BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREHIS B:55 , HIS B:57 , LYS B:169 , ASP B:301 , ZN B:403 , HOH B:721BINDING SITE FOR RESIDUE ZN B 401
5AC5SOFTWAREHIS B:201 , HIS B:230 , ZN B:403 , HLN B:404 , HOH B:721BINDING SITE FOR RESIDUE ZN B 402
6AC6SOFTWAREHIS B:55 , HIS B:230 , ASP B:301 , ZN B:401 , ZN B:402 , HLN B:404 , HOH B:721BINDING SITE FOR RESIDUE ZN B 403
7AC7SOFTWAREHIS B:55 , HIS B:57 , TRP B:131 , LYS B:169 , HIS B:201 , GLY B:204 , HIS B:230 , ARG B:254 , PHE B:271 , ASP B:301 , ILE B:306 , SER B:308 , ZN B:402 , ZN B:403 , HOH B:721BINDING SITE FOR RESIDUE HLN B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E3T)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4E3T)

(-) 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:327
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:327
                                    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       335       345       355       
            OPD_BREDI    36 RINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTL 362
               SCOP domains d4e3ta_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeehhhhh..eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eeee....hhhhhh.hhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..hhh.eeeehhhhh.hhhhhhhhhhh..eeee.hhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PHOSPHOTR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e3t A  36 RINTVRGPITISEVGFTLTHEHICGSSAGFLRAWPEFFGSREALVEKAVRGLRRARAAGVRTIVDVSTFDLGRDVRLLAEVSRAADVHIVAATGVWLDPPLSIRMRSVEELTQFFLREIQYGIEDTGIRAGIIKVAITGKVTPFQELVLRAAARASLATGVPVITHTAGSQRGGEQQAAIFESEGLSPSRVCIGHSDETDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASATAFMGSRSWQTRALLIKALIDQGYMKQILVSNDWLFGISSYVTNFMDVMDSVNPDGMAFIPLRVIPFLREKGIPQETLAGITVTNPARFLSPTL 362
                                    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       335       345       355       


Chain B from PDB  Type:PROTEIN  Length:326
 aligned with OPD_BREDI | P0A434 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:326
                                    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       335       345       355      
            OPD_BREDI    36 RINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPT 361
               SCOP domains d4e3tb_ B: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeehhhhhh.eeeee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhh.eee.eeee....hhhhhh.hhhhhhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhhh..eeee............hhhhhhhhh..hhhhhhhhhhhhhhh.hhh.eee......ee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PHOSPHOTR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e3t B  36 RINTVRGPITISEVGFTLTHEHICGSSAGFLRAWPEFFGSREALVEKAVRGLRRARAAGVRTIVDVSTFDLGRDVRLLAEVSRAADVHIVAATGVWLDPPLSIRMRSVEELTQFFLREIQYGIEDTGIRAGIIKVAITGKVTPFQELVLRAAARASLATGVPVITHTAGSQRGGEQQAAIFESEGLSPSRVCIGHSDETDDLSYLTALAARGYLIGLDRIPHSAIGLEDNASATAFMGSRSWQTRALLIKALIDQGYMKQILVSNDWLFGISSYVTNFMDVMDSVNPDGMAFIPLRVIPFLREKGIPQETLAGITVTNPARFLSPT 361
                                    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       335       345       355
   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  (0, 0)

(no "CATH Domain" information available for 4E3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E3T)

(-) 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 1i0d 1jgm 1psc 1pta 1qw7 2o4m 2o4q 2ob3 2oql 3cak 3cs2 3e3h 3upm 3ur2 3ur5 3ura 3urb 3urn 3urq 4gy0 4gy1 4zst 4zsu

(-) Related Entries Specified in the PDB File

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