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(-) Description

Title :  SERUM PARAOXONASE BY DIRECTED EVOLUTION
 
Authors :  M. Harel, A. Aharoni, L. Gaidukov, B. Brumshtein, O. Khersonsky, S. Yag R. Meged, H. Dvir, R. B. G. Ravelli, A. Mccarthy, L. Toker, I. Silman, J. L. Sussman, D. S. Tawfik
Date :  22 Mar 04  (Deposition) - 23 Apr 04  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Paraoxonase, Hydrolase, Directed Evolution, Antioxidant, Israel Structural Proteomics Center, Ispc, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Harel, A. Aharoni, L. Gaidukov, B. Brumshtein, O. Khersonsky, R. Meged, H. Dvir, R. B. G. Ravelli, A. Mccarthy, L. Toker, I. Silman, J. L. Sussman, D. S. Tawfik
Structure And Evolution Of The Serum Paraoxonase Family Of Detoxifying And Anti-Atherosclerotic Enzymes
Nat. Struct. Mol. Biol. V. 11 412 2004
PubMed-ID: 15098021  |  Reference-DOI: 10.1038/NSMB767

(-) Compounds

Molecule 1 - SERUM PARAOXONASE/ARYLESTERASE 1
    ChainsA
    EC Number3.1.1.2, 3.1.8.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 32B(+)
    Expression System StrainORIGAMI B (DE3)
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS, ORYCTOLAGUS CUNICULUS, MUS MUSCULUS, RATTUS RATTUS
    Organism Taxid9606, 9986, 10090, 10117
    Other DetailsPARAOXONASE-1 (PON1)
    Other Details - SourceFROM SHUFFLED GENES OF HUMAN, RABBIT, MOUSE AND RAT PARAOXONASE
    SynonymA-ESTERASE 1, SERUM ARYLDIALKYLPHOSPHATASE 1, PON1, AROMATIC ESTERASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:54 , ILE A:117 , ASP A:169 , HOH A:2010 , HOH A:2011 , HOH A:2053BINDING SITE FOR RESIDUE CA A1356
2AC2SOFTWAREGLU A:53 , ASN A:168 , ASN A:224 , ASP A:269 , ASN A:270 , PO4 A:1358 , HOH A:2009BINDING SITE FOR RESIDUE CA A1357
3AC3SOFTWAREGLU A:53 , HIS A:115 , ASN A:168 , ASN A:224 , ASP A:269 , THR A:332 , VAL A:346 , CA A:1357BINDING SITE FOR RESIDUE PO4 A1358

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:353

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006043L55MPON1_HUMANPolymorphism854560AL55M
2UniProtVAR_015882I102VPON1_HUMANPolymorphism72552787AI102V
3UniProtVAR_055342R160GPON1_HUMANPolymorphism13306698AR160G
4UniProtVAR_006044Q192RPON1_HUMANPolymorphism662AK192R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V04)

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002223811aENSE00000877451chr7:94954019-94953714306PON1_HUMAN1-25251A:16-2510
1.2bENST000002223812bENSE00000434428chr7:94947705-9494763571PON1_HUMAN25-49251A:25-4925
1.3ENST000002223813ENSE00000706211chr7:94946101-9494604656PON1_HUMAN49-67191A:49-6719
1.4aENST000002223814aENSE00000706210chr7:94944802-94944634169PON1_HUMAN68-124571A:68-124 (gaps)57
1.5bENST000002223815bENSE00001620379chr7:94940889-94940763127PON1_HUMAN124-166431A:124-16643
1.6ENST000002223816ENSE00001622965chr7:94937523-94937323201PON1_HUMAN166-233681A:166-23368
1.7ENST000002223817ENSE00001662155chr7:94935678-9493559782PON1_HUMAN233-260281A:233-26028
1.8bENST000002223818bENSE00001748242chr7:94931645-94931517129PON1_HUMAN261-303431A:261-30343
1.9cENST000002223819cENSE00001182780chr7:94928414-949269881427PON1_HUMAN304-355521A:304-35552

(-) 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:332
 aligned with PON1_HUMAN | P27169 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:340
                                    25        35        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
           PON1_HUMAN    16 LFRNHQSSYQTRLNALREVQPVELPNCNLVKGIETGSEDLEILPNGLAFISSGLKYPGIKSFNPNSPGKILLMDLNEEDPTVLELGITGSKFDVSSFNPHGISTFTDEDNAMYLLVVNHPDAKSTVELFKFQEEEKSLLHLKTIRHKLLPNLNDIVAVGPEHFYGTNDHYFLDPYLQSWEMYLGLAWSYVVYYSPSEVRVVAEGFDFANGINISPDGKYVYIAELLAHKIHVYEKHANWTLTPLKSLDFNTLVDNISVDPETGDLWVGCHPNGMKIFFYDSENPPASEVLRIQNILTEEPKVTQVYAENGTVLQGSTVASVYKGKLLIGTVFHKALYCEL 355
               SCOP domains d1v04a_ A: Serum paraoxonase/arylesterase 1, PON1                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1v04A00 A:16-355 TolB, C-terminal domain                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..............ee.........eeee....eeeeee....--------....eeeeee.......eee.eee....hhhhh.eeeeeeee.....eeeeeee......eeeeeeee....eeeeeeee.......eeeeeeee..eeeeee.....hhhhhhhhhhh....eeeeee....eeeeeeee..eeeeee.....eeeeee....eeeeeee.....eeeeeeee...eeeeeee......eeeeee.hhhhhhh........eeeeeee.......eeeeeeee.......eeeeeee..eeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------M----------------------------------------------V---------------------------------------------------------G-------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a -----------------------Exon 1.3           Exon 1.4a  PDB: A:68-124 (gaps) UniProt: 68-124          -----------------------------------------Exon 1.6  PDB: A:166-233 UniProt: 166-233                           ---------------------------Exon 1.8b  PDB: A:261-303 UniProt: 261-303 Exon 1.9c  PDB: A:304-355 UniProt: 304-355           Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.2b  PDB: A:25-49  --------------------------------------------------------------------------Exon 1.5b  PDB: A:124-166 UniProt: 124-166 ------------------------------------------------------------------Exon 1.7  PDB: A:233-260    ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1v04 A  16 LFDRQKSSFQTRFNVHREVTPVELPNCNLVKGIDNGSEDLEILPNGLAFISSGLKY--------DKSGKILLMDLNEKEPAVSELEIIGNTLDISSFNPHGISTFIDDDNTVYLLVVNHPGSSSTVEVFKFQEEEKSLLHLKTIRHKLLPSVNDIVAVGPEHFYATNDHYFIDPYLKSWEMHLGLAWSFVTYYSPNDVRVVAEGFDFANGINISPDGKYVYIAELLAHKIHVYEKHANWTLTPLRVLSFDTLVDNISVDPVTGDLWVGCHPNGMRIFFYDAENPPGSEVLRIQDILSEEPKVTVVYAENGTVLQGSTVAAVYKGKLLIGTVFHKALYCDL 355
                                    25        35        45        55        65     |   -    |   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
                                                                                  71       80                                                                                                                                                                                                                                                                                   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V04)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PON1_HUMAN | P27169)
molecular function
    GO:0102007    acyl-L-homoserine-lactone lactonohydrolase activity    Catalysis of the reaction: H2O + an N-acyl-L-homoserine lactone <=> H+ + an N-acyl-L-homoserine.
    GO:0004063    aryldialkylphosphatase activity    Catalysis of the reaction: aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol.
    GO:0004064    arylesterase activity    Catalysis of the reaction: a phenyl acetate + H2O = a phenol + acetate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0046395    carboxylic acid catabolic process    The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0034445    negative regulation of plasma lipoprotein oxidation    Any process that stops, prevents, or reduces the frequency, rate or extent of lipoprotein particle oxidation, occurring in the blood plasma.
    GO:0046434    organophosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound.
    GO:0046470    phosphatidylcholine metabolic process    The chemical reactions and pathways involving phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline. They are important constituents of cell membranes.
    GO:0051099    positive regulation of binding    Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
    GO:0010875    positive regulation of cholesterol efflux    Any process that increases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    GO:0032411    positive regulation of transporter activity    Any process that activates or increases the activity of a transporter.
    GO:0009605    response to external stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
    GO:0070542    response to fatty acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:1902617    response to fluoride    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluoride stimulus.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0034364    high-density lipoprotein particle    A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0034366    spherical high-density lipoprotein particle    A mature high-density lipoprotein (HDL) particle, converted from discoidal HDL particles following the esterification of cholesterol in the particle by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT).

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 Related Entries

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

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        PON1_HUMAN | P271691xhr

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