1FGR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   LIPOXYGENASE-1 (SOYBEAN) AT 100K, Q697E MUTANT

Authors :   D. R. Tomchick, W. Minor, T. Holman

Date :   28 Jul 00 (Deposition) - 04 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Dioxygenase, Lipoxygenase, Metalloprotein, Fatty Acids, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Tomchick, P. Phan, M. Cymborowski, W. Minor, T. R. Holman
Structural And Functional Characterization Of Second-Coordination Sphere Mutants Of Soybean Lipoxygenase-1.
Biochemistry V. 40 7509 2001
PubMed-ID: 11412104 | Reference-DOI: 10.1021/BI002893D
(for further references see the PDB file header)

Molecule 1 - SEED LIPOXYGENASE-1
	Chains	:	A
	EC Number	:	1.13.11.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	SOYBEAN
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847
	Synonym	:	L-1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	FE	1	Ligand/Ion	FE (III) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:499 , HIS A:504 , HIS A:690 , ASN A:694 , ILE A:839 , HOH A:1429	BINDING SITE FOR RESIDUE FE A 840

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:365	-	Pro A:366

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLAT	PS50095	PLAT domain profile.	LOX1_SOYBN	16-145	1	A:16-145
2	LIPOXYGENASE_3	PS51393	Lipoxygenase iron-binding catalytic domain profile.	LOX1_SOYBN	148-839	1	A:148-839
3	LIPOXYGENASE_1	PS00711	Lipoxygenases iron-binding region signature 1.	LOX1_SOYBN	494-508	1	A:494-508
4	LIPOXYGENASE_2	PS00081	Lipoxygenases iron-binding region signature 2.	LOX1_SOYBN	521-531	1	A:521-531

(no "Exon" information available for 1FGR)

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:821
 aligned with LOX1_SOYBN | P08170 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:834
                                    15        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       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835    
           LOX1_SOYBN     6 HKIKGTVVLMPKNELEVNPDGSAVDNLNAFLGRSVSLQLISATKADAHGKGKVGKDTFLEGINTSLPTLGAGESAFNIHFEWDGSMGIPGAFYIKNYMQVEFFLKSLTLEAISNQGTIRFVCNSWVYNTKLYKSVRIFFANHTYVPSETPAPLVSYREEELKSLRGNGTGERKEYDRIYDYDVYNDLGNPDKSEKLARPVLGGSSTFPYPRRGRTGRGPTVTDPNTEKQGEVFYVPRDENLGHLKSKDALEIGTKSLSQIVQPAFESAFDLKSTPIEFHSFQDVHDLYEGGIKLPRDVISTIIPLPVIKELYRTDGQHILKFPQPHVVQVSQSAWMTDEEFAREMIAGVNPCVIRGLEEFPPKSNLDPAIYGDQSSKITADSLDLDGYTMDEALGSRRLFMLDYHDIFMPYVRQINQLNSAKTYATRTILFLREDGTLKPVAIELSLPHSAGDLSAAVSQVVLPAKEGVESTIWLLAKAYVIVNDSCYHQLMSHWLNTHAAMEPFVIATHRHLSVLHPIYKLLTPHYRNNMNINALARQSLINANGIIETTFLPSKYSVEMSSAVYKNWVFTDQALPADLIKRGVAIKDPSTPHGVRLLIEDYPYAADGLEIWAAIKTWVQEYVPLYYARDDDVKNDSELQHWWKEAVEKGHGDLKDKPWWPKLQTLEDLVEVCLIIIWIASALHAAVNFGQYPYGGLIMNRPTASRRLLPEKGTPEYEEMINNHEKAYLRTITSKLPTLISLSVIEILSTHASDEVYLGQRDNPHWTSDSKALQAFQKFGNKLKEIEEKLVRRNNDPSLQGNRLGPVQLPYTLLYPSSEEGLTFRGIPNSISI 839
               SCOP domains d1fgra2 A:6-149          Plant lipoxigenase                                                                                                     d1fgra1 A:150-839 Lipoxigenase, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---1fgrA01 A:9-1         67 Lipoxygenase-1                                                                                                                        1fgrA02 A:168-267 Lipoxygenase-1; Domain 2                                                          1fgrA03 A:268-356 Lipoxygenase-1; Domain 3                                               1fgrA04 A:357-490  [code=3.10.450.60, no name defined]                                                                                1fgrA05 A:491-837 Lipoxygenase-1; Domain 5                                                                                                                                                                                                                                                                                                                 -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.hhh.---------hhhhhh...eeeeeeeeeee.....eee...ee..eee..........eeeeeeee.hhhhh.eeeeeeee.....eeeeeeee...----.eeeeeeeee..hhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh..............ee..........hhhhh..............ee......................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..ee.hhhhhhhhh...hhhhh.ee....eee...hhhhh...hhhhhhhhhhhhhhhh......ee..........hhhhhh......hhhhh.....hhhhhhhh..eeeeehhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeee.............eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eee....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------PLAT  PDB: A:16-145 UniProt: 16-145                                                                                               --LIPOXYGENASE_3  PDB: A:148-839 UniProt: 148-839                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LIPOXYGENASE_1 ------------LIPOXYGENAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fgr A   6 HKIKGTVVLMPKNELE---------NLNAFLGRSVSLQLISATKADAHGKGKVGKDTFLEGINTSLPTLGAGESAFNIHFEWDGSMGIPGAFYIKNYMQVEFFLKSLTLEAI----TIRFVCNSWVYNTKLYKSVRIFFANHTYVPSETPAPLVSYREEELKSLRGNGTGERKEYDRIYDYDVYNDLGNPDKSEKLARPVLGGSSTFPYPRRGRTGRGPTVTDPNTEKQGEVFYVPRDENLGHLKSKDALEIGTKSLSQIVQPAFESAFDLKSTPIEFHSFQDVHDLYEGGIKLPRDVISTIIPLPVIKELYRTDGQHILKFPQPHVVQVSQSAWMTDEEFAREMIAGVNPCVIRGLEEFPPKSNLDPAIYGDQSSKITADSLDLDGYTMDEALGSRRLFMLDYHDIFMPYVRQINQLNSAKTYATRTILFLREDGTLKPVAIELSLPHSAGDLSAAVSQVVLPAKEGVESTIWLLAKAYVIVNDSCYHQLMSHWLNTHAAMEPFVIATHRHLSVLHPIYKLLTPHYRNNMNINALARQSLINANGIIETTFLPSKYSVEMSSAVYKNWVFTDQALPADLIKRGVAIKDPSTPHGVRLLIEDYPYAADGLEIWAAIKTWVQEYVPLYYARDDDVKNDSELQHWWKEAVEKGHGDLKDKPWWPKLQTLEDLVEVCLIIIWIASALHAAVNFGEYPYGGLIMNRPTASRRLLPEKGTPEYEEMINNHEKAYLRTITSKLPTLISLSVIEILSTHASDEVYLGQRDNPHWTSDSKALQAFQKFGNKLKEIEEKLVRRNNDPSLQGNRLGPVQLPYTLLYPSSEEGLTFRGIPNSISI 839
                                    15     |   -     |  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       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835    
                                          21        31                                                                                   117  122

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 "Pfam Domain" information available for 1FGR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LOX1_SOYBN | P08170)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0016165	linoleate 13S-lipoxygenase activity	Catalysis of the reaction: linoleate + O2 = (9Z,11E)-(13S)-13-hydroperoxyoctadeca-9,11-dienoate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0031408	oxylipin biosynthetic process	The chemical reactions and pathways resulting in the formation of any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:365 - Pro A:366	[ RasMol ]

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	1fgr
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	LOX1_SOYBN \| P08170
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	1.13.11.12
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1f8n	1F8N IS LIPOXYGENASE-1 (SOYBEAN), NEW REFINEMENT
1fgm	1FGM IS LIPOXYGENASE-1 (SOYBEAN), N694H MUTANT
1fgo	1FGO IS LIPOXYGENASE-1 (SOYBEAN), Q495A MUTANT
1fgq	1FGQ IS LIPOXYGENASE-1 (SOYBEAN), Q495E MUTANT
1fgt	1FGT IS LIPOXYGENASE-1 (SOYBEAN), Q697N MUTANT
1yge	1YGE IS LIPOXYGENASE-1 (SOYBEAN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (5, 5)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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