1XHR - JenaLib

Theoretical Model (Jmol Viewer)

Title :   HUMAN PARAOXONASE 1 BY HOMOLOGY TO DFPASE

Authors :   J. D. Nicholson, D. Josse

Date :   20 Sep 04 (Deposition) - 12 Oct 04 (Release) - 12 Oct 04 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Paraoxonase, Human Paraoxonase, Human Serum Paraoxonase, Pon Calcium-Binding Site, Beta-Propeller (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. T. Yeung, D. Josse, J. D. Nicholson, A. Khanal, C. W. Mcandrew, B. J. Bahnson, D. E. Lenz, D. M. Cerasoli
Structure/Function Analyses Of Human Serum Paraoxonase (Hupon1) Mutants Designed From A Dfpase-Like Homology Model
Biochim. Biophys. Acta V. 1702 67 2004
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SERUM PARAOXONASE/ARYLESTERASE 1
	Chains	:	A
	EC Number	:	3.1.1.2, 3.1.8.1
	Fragment	:	RESIDUES 40-355
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	SERUM PARAOXONASE 1, PON 1, SERUM ARYLDIALKYLPHOSPHATASE 1, A-ESTERASE 1, AROMATIC ESTERASE 1, K-45


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

(no "Site" information available for 1XHR)

Theoretical Model

No.	Residues
1	A:42	-	A:353

Theoretical Model

No.	Residues
1	Asn A:78	-	Pro A:79
2	Asp A:188	-	Pro A:189
3	Asp A:231	-	Gly A:232
4	Thr A:277	-	Gly A:278

Theoretical Model (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006043	L	55	M	PON1_HUMAN	Polymorphism	854560	A	M	55	M
2	UniProt	VAR_015882	I	102	V	PON1_HUMAN	Polymorphism	72552787	A	I	102	V
3	UniProt	VAR_055342	R	160	G	PON1_HUMAN	Polymorphism	13306698	A	R	160	G
4	UniProt	VAR_006044	Q	192	R	PON1_HUMAN	Polymorphism	662	A	Q	192	R

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

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

Theoretical Model (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000222381	1a	ENSE00000877451	chr7:94954019-94953714	306	PON1_HUMAN	1-25	25	0	-	-
1.2b	ENST00000222381	2b	ENSE00000434428	chr7:94947705-94947635	71	PON1_HUMAN	25-49	25	1	A:40-49	10
1.3	ENST00000222381	3	ENSE00000706211	chr7:94946101-94946046	56	PON1_HUMAN	49-67	19	1	A:49-67	19
1.4a	ENST00000222381	4a	ENSE00000706210	chr7:94944802-94944634	169	PON1_HUMAN	68-124	57	1	A:68-124	57
1.5b	ENST00000222381	5b	ENSE00001620379	chr7:94940889-94940763	127	PON1_HUMAN	124-166	43	1	A:124-166	43
1.6	ENST00000222381	6	ENSE00001622965	chr7:94937523-94937323	201	PON1_HUMAN	166-233	68	1	A:166-233	68
1.7	ENST00000222381	7	ENSE00001662155	chr7:94935678-94935597	82	PON1_HUMAN	233-260	28	1	A:233-260	28
1.8b	ENST00000222381	8b	ENSE00001748242	chr7:94931645-94931517	129	PON1_HUMAN	261-303	43	1	A:261-303	43
1.9c	ENST00000222381	9c	ENSE00001182780	chr7:94928414-94926988	1427	PON1_HUMAN	304-355	52	1	A:304-355	52

Theoretical Model

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:316
 aligned with PON1_HUMAN | P27169 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:316
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349      
           PON1_HUMAN    40 PNCNLVKGIETGSEDLEILPNGLAFISSGLKYPGIKSFNPNSPGKILLMDLNEEDPTVLELGITGSKFDVSSFNPHGISTFTDEDNAMYLLVVNHPDAKSTVELFKFQEEEKSLLHLKTIRHKLLPNLNDIVAVGPEHFYGTNDHYFLDPYLQSWEMYLGLAWSYVVYYSPSEVRVVAEGFDFANGINISPDGKYVYIAELLAHKIHVYEKHANWTLTPLKSLDFNTLVDNISVDPETGDLWVGCHPNGMKIFFYDSENPPASEVLRIQNILTEEPKVTQVYAENGTVLQGSTVASVYKGKLLIGTVFHKALYCEL 355
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee.....eeee..................eeeee....eeee..................eeee.......eeeeee....eeeee............................eee.....eeeee..................eeeee...........eeee.....ee......eeeeee....eeeeee....................ee.........eee........ee......................eeeee.......eeeee.....eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------M----------------------------------------------V---------------------------------------------------------G-------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b ------------------Exon 1.4a  PDB: A:68-124 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 1.3           --------------------------------------------------------Exon 1.5b  PDB: A:124-166 UniProt: 124-166 ------------------------------------------------------------------Exon 1.7  PDB: A:233-260    ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1xhr A  40 PNCNLVKGIETGSEDMEILPNGLAFISSGLKYPGIKSFNPNSPGKILLMDLNEEDPTVLELGITGSKFDVSSFNPHGISTFTDEDNAMYLLVVNHPDAKSTVELFKFQEEEKSLLHLKTIRHKLLPNLNDIVAVGPEHFYGTNDHYFLDPYLQSWEMYLGLAWSYVVYYSPSEVRVVAEGFDFANGINISPDGKYVYIAELLAHKIHVYEKHANWTLTPLKSLDFNTLVDNISVDPETGDLWVGCHPNGMKIFFYDSENPPASEVLRIQNILTEEPKVTQVYAENGTVLQGSTVASVYKGKLLIGTVFHKALYCEL 355
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349

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 '\|'

(no "SCOP Domain" information available for 1XHR)

(no "CATH Domain" information available for 1XHR)

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

Theoretical Model(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).

Theoretical Model
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	Cis Peptide Bonds
		Asn A:78 - Pro A:79	[ RasMol ]
		Asp A:188 - Pro A:189	[ RasMol ]
		Asp A:231 - Gly A:232	[ RasMol ]
		Thr A:277 - Gly A:278	[ RasMol ]

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	PON1_HUMAN \| P27169	:	1v04

(no "Related Entries Specified in the PDB File" available for 1XHR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (0, 0)

Exons (8, 8)

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