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Title :   CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE-B

Authors :   B. Youn, G. E. Sellhorn, R. J. Mirchel, B. J. Gaffney, H. D. Grimes, C. Kang

Date :   05 Jun 06 (Deposition) - 11 Oct 06 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Dioxygenase, Metal-Binding, Oxidoreductase, Soybean Lipoxygenase-B, Fatty Acid Biosynthesis, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Youn, G. E. Sellhorn, R. J. Mirchel, B. J. Gaffney, H. D. Grimes, C. Kang
Crystal Structures Of Vegetative Soybean Lipoxygenase Vlx-B And Vlx-D, And Comparisons With Seed Isoforms Lox-1 And Lox-3.
Proteins V. 65 1008 2006
PubMed-ID: 17022084 | Reference-DOI: 10.1002/PROT.21182

Molecule 1 - LIPOXYGENASE L-5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	SOYBEAN
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847
	Synonym	:	VEGETATIVE LIPOXYGENASE-B

		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:513 , HIS A:518 , HIS A:704 , ASN A:708 , ILE A:853	BINDING SITE FOR RESIDUE FE A1854

(no "SS Bond" information available for 2IUJ)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:475	-	Pro A:476

(no "SAP(SNP)/Variant" information available for 2IUJ)

(no "PROSITE Motif" information available for 2IUJ)

(no "Exon" information available for 2IUJ)

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:833
 aligned with Q43446_SOYBN | Q43446 from UniProtKB/TrEMBL  Length:853

    Alignment length:846
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847      
         Q43446_SOYBN     8 GQKIKGTMVVMQKNVLDINSITSVDGIVGTGLDFLGSALDTVTFLASSISIQLISATKADGGKGKVGKATNLRGKITLPTIGAKEEAYDAQFDWDSDFGIPGAFYIKNYMQNEFYLKSLILEDIPNHGTIHFICNSWVYNSKHYKTDRIFFANNTYLPSETPAPLVKYREEELKNVRGDGTGERKEWDRIYDYDVYNDLGDPDKGEKYARPVLGGSALPYPRRGRTGRGKTRKDPNSEKPGDFVYLPRDEAFGHLKSSDFLAYGIKSVAQDVLPVLTDAFDGNLLSLDFDNFAEVRKLYEGGVTLPTNFLSNITPIPIIKELFRTDGEQFLKYPPPKVMQVDKSAWMTDEEFARETIAGLNPNVIKIIEEFPLSSKLDTQAYGDHTCIITKEHLEPNLGGLTVEQAIQNKKLFILDHHDYLIPYLRKINANTTKTYATRTIFFLKNDGTLTPLAIELSKPHPQGEEYGPVSEVYVPSSEGVEAYIWLLAKAYVVVNDACYHQIISHWLNTHAVVEPFVIATNRHLSVVHPIYKLLFPHYRDTMNINSLARKSLVNADGIIEKTFLWGRYSLEMSAVIYKDWVFTDQALPNDLVKRGVAVKDPSAPHGVRLLIEDYPYASDGLEIWDAIKSWVEEYVSFYYKSDEELQKDPELQAWWKELVEVGHGDLKDKPWWQKMQTREELVEASATLIWIASALHAAVNFGQYPYGGLILNRPTISRRFMPEKGSPEYDALAKNPEKEFLKTITGKKETLIDLTIIEILSRHASDEFYLGQRDGGDYWTSDAGPLEAFKRFGKNLEEIEKKLIEKNNDETLRNRYGPAKMPYTLLYPSSEEGLTFRGIPNSISI 853
               SCOP domains d2iuja1 A:8-163 automate             d matches                                                                                                              d2iuja2 A:164-853 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2iujA01 A:8-163 Lipoxyge             nase-1                                                                                                                 2iujA02 A:164-262 Lipoxygenase-1; Domain 2                                                         2iujA03 A:263-351 Lipoxygenase-1; Domain 3                                               2iujA04 A:352-485  [code=3.10.450.60, no name defined]                                                                                2iujA05 A:486-852 Lipoxygenase-1; Domain 5                                                                                                                                                                                                                                                                                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhh........-------------...........eeeeeeeeeee....eeeeeeee..............eeeeeeee.......eeeeeeee.....eeeeeeee........eeeeeeeee.........eeee.....hhhhh...hhhhhhhhhhhhhh..............ee......hhhhh.................ee......................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhh......................hhhhh.......hhhhhhhh..........ee..................................hhhhhhhh..eee......hhhhhhhhhh.........eeeee.....eeeeeeeeee....hhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.eee.......eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.................hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iuj A   8 GQKIKGTMVVMQKNVLDINSITSV-------------ALDTVTFLASSISIQLISATKADGGKGKVGKATNLRGKITLPTIGAKEEAYDAQFDWDSDFGIPGAFYIKNYMQNEFYLKSLILEDIPNHGTIHFICNSWVYNSKHYKTDRIFFANNTYLPSETPAPLVKYREEELKNVRGDGTGERKEWDRIYDYDVYNDLGDPDKGEKYARPVLGGSALPYPRRGRTGRGKTRKDPNSEKPGDFVYLPRDEAFGHLKSSDFLAYGIKSVAQDVLPVLTDAFDGNLLSLDFDNFAEVRKLYEGGVTLPTNFLSNITPIPIIKELFRTDGEQFLKYPPPKVMQVDKSAWMTDEEFARETIAGLNPNVIKIIEEFPLSSKLDTQAYGDHTCIITKEHLEPNLGGLTVEQAIQNKKLFILDHHDYLIPYLRKINANTTKTYATRTIFFLKNDGTLTPLAIELSKPHPQGEEYGPVSEVYVPSSEGVEAYIWLLAKAYVVVNDACYHQIISHWLNTHAVVEPFVIATNRHLSVVHPIYKLLFPHYRDTMNINSLARKSLVNADGIIEKTFLWGRYSLEMSAVIYKDWVFTDQALPNDLVKRGVAVKDPSAPHGVRLLIEDYPYASDGLEIWDAIKSWVEEYVSFYYKSDEELQKDPELQAWWKELVEVGHGDLKDKPWWQKMQTREELVEASATLIWIASALHAAVNFGQYPYGGLILNRPTISRRFMPEKGSPEYDALAKNPEKEFLKTITGKKETLIDLTIIEILSRHASDEFYLGQRDGGDYWTSDAGPLEAFKRFGKNLEEIEKKLIEKNNDETLRNRYGPAKMPYTLLYPSSEEGLTFRGIPNSISI 853
                                    17        27   |     -       |47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847      
                                                  31            45

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Lipoxigenase (27)

Superfamily: Lipoxigenase (27)

Family: Plant lipoxigenases (25)

Protein domain: automated matches (2)

Soybean (Glycine max) [TaxId: 3847] (2)

d2iuja2

A:164-853

Class: All beta proteins (24004)

Fold: Lipase/lipooxygenase domain (PLAT/LH2 domain) (47)

Superfamily: Lipase/lipooxygenase domain (PLAT/LH2 domain) (47)

Family: automated matches (8)

Protein domain: automated matches (8)

Soybean (Glycine max) [TaxId: 3847] (2)

d2iuja1

A:8-163

(no "Pfam Domain" information available for 2IUJ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q43446_SOYBN | Q43446)

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: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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:475 - Pro A:476	[ RasMol ]

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2iuk	CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE-D

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 (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (5, 5)

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Gene Ontology (7, 7)

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