2GIN - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE WT ALLENE OXIDE CYCLASE 2 FROM ARABIDOPSIS THALIANA

Authors :   E. Hofmann, F. Schaller, P. Zerbe

Date :   29 Mar 06 (Deposition) - 21 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Beta Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Hofmann, P. Zerbe, F. Schaller
The Crystal Structure Of Arabidopsis Thaliana Allene Oxide Cyclase: Insights Into The Oxylipin Cyclization Reaction
Plant Cell V. 18 3201 2006
PubMed-ID: 17085685 | Reference-DOI: 10.1105/TPC.106.043984

Molecule 1 - ALLENE OXIDE CYCLASE 2
	Chains	:	A, B, C, D, E, F
	EC Number	:	5.3.99.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ALLENE OXIDE CYCLASE 2
	Gene	:	AT3G25770
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:37 , HOH A:1000 , HOH A:1001 , LEU B:35 , ASN B:37 , LEU C:35 , ASN C:37	BINDING SITE FOR RESIDUE GOL A 901
2	AC2	SOFTWARE	LEU D:35 , ASN D:37 , HOH D:951 , HOH D:982 , ASN E:37 , HOH E:294 , ASN F:37	BINDING SITE FOR RESIDUE GOL D 902
3	AC3	SOFTWARE	PRO F:32 , CYS F:71 , TYR F:136 , HOH F:986 , HOH F:1000	BINDING SITE FOR RESIDUE GOL F 903
4	AC4	SOFTWARE	ASN B:53 , HOH B:980	BINDING SITE FOR RESIDUE GOL B 904
5	AC5	SOFTWARE	ASP D:28 , ARG D:29 , LYS D:54 , ASN D:188	BINDING SITE FOR RESIDUE GOL D 905

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

Asymmetric Unit

No.	Residues
1	Ser A:31	-	Pro A:32
2	Tyr A:136	-	Pro A:137
3	Ser B:31	-	Pro B:32
4	Tyr B:136	-	Pro B:137
5	Ser C:31	-	Pro C:32
6	Tyr C:136	-	Pro C:137
7	Ser D:31	-	Pro D:32
8	Tyr D:136	-	Pro D:137
9	Ser E:31	-	Pro E:32
10	Tyr E:136	-	Pro E:137
11	Ser F:31	-	Pro F:32
12	Tyr F:136	-	Pro F:137

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

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

(no "Exon" information available for 2GIN)

Asymmetric 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:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gina_ A: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin A  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginb_ B: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin B  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginc_ C: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin C  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain D from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gind_ D: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin D  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain E from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gine_ E: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin E  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain F from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginf_ F: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhhh...........hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin F  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: AOC barrel-like (13)

Superfamily: Allene oxide cyclase-like (11)

Family: Allene oxide cyclase-like (9)

Protein domain: Allene oxide cyclase, AOC (6)

Thale cress (Arabidopsis thaliana), chloroplast AOC2 [TaxId: 3702] (5)

1a	d2gina_	A:
1b	d2ginb_	B:
1c	d2ginc_	C:
1d	d2gind_	D:
1e	d2gine_	E:
1f	d2ginf_	F:

(no "CATH Domain" information available for 2GIN)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (AOC2_ARATH | Q9LS02)

molecular function
	GO:0046423	allene-oxide cyclase activity	Catalysis of the reaction: (9Z,13S,15Z)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0009695	jasmonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
	GO:0009409	response to cold	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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009941	chloroplast envelope	The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
	GO:0009570	chloroplast stroma	The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0010319	stromule	Thin filamentous structure extending from the surface of all plastid types examined so far, including chloroplast, proplastid, etioplast, leucoplast, amyloplast, and chromoplast. In general, stromules are more abundant in tissues containing non-green plastids, and in cells containing smaller plastids. The primary function of stromules is still unresolved, although the presence of stromules markedly increases the plastid surface area, potentially increasing transport to and from the cytosol. Other functions of stromules, such as transfer of macromolecules between plastids and starch granule formation in cereal endosperm, may be restricted to particular tissues and cell types.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Ser A:31 - Pro A:32	[ RasMol ]
		Ser B:31 - Pro B:32	[ RasMol ]
		Ser C:31 - Pro C:32	[ RasMol ]
		Ser D:31 - Pro D:32	[ RasMol ]
		Ser E:31 - Pro E:32	[ RasMol ]
		Ser F:31 - Pro F:32	[ RasMol ]
		Tyr A:136 - Pro A:137	[ RasMol ]
		Tyr B:136 - Pro B:137	[ RasMol ]
		Tyr C:136 - Pro C:137	[ RasMol ]
		Tyr D:136 - Pro D:137	[ RasMol ]
		Tyr E:136 - Pro E:137	[ RasMol ]
		Tyr F:136 - Pro F:137	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2gin
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	AOC2_ARATH \| Q9LS02
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	5.3.99.6
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	AOC2_ARATH \| Q9LS02
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	AOC2_ARATH \| Q9LS02	:	1z8k 2brj 2dio 2q4i 4cq6 4cq7

1z8k	STRUCTURE OF AOC2 SOLVED BY THE CESG STRUCTURAL GENOMICS CONSORTIUM
2brj	HIGHER RESOLUTION STRUCTURE WITH SEMET SUBSTITUTION FOR PHASING
2dio	THE SAME PROTEIN COMPLEXED WITH INHIBITOR VERNOLIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

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Gene Ontology (10, 10)

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