4H69 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ALLENE OXIDE CYCLASE 2 FROM PHYSCOMITRELLA PATENS COMPLEXED WITH SUBSTRATE ANALOG

Authors :   P. Neumann, R. Ficner

Date :   19 Sep 12 (Deposition) - 17 Oct 12 (Release) - 12 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   B-Barrel, Oxylipins, Fatty Acid, Metabolites, Allene-Oxide Cyclase Activity, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Neumann, F. Brodhun, K. Sauer, C. Herrfurth, M. Hamberg, J. Brinkmann, J. Scholz, A. Dickmanns, I. Feussner, R. Ficner
Crystal Structures Of Physcomitrella Patens Aoc1 And Aoc2: Insights Into The Enzyme Mechanism And Differences In Substrate Specificity.
Plant Physiol. V. 160 1251 2012
PubMed-ID: 22987885 | Reference-DOI: 10.1104/PP.112.205138

Molecule 1 - ALLENE OXIDE CYCLASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	5.3.99.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6-P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AOC2
	Organism Scientific	:	PHYSCOMITRELLA PATENS
	Organism Taxid	:	3218

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	10Y	5	Ligand/Ion	(9Z)-11-{(2R,3S)-3-[(2Z)-PENT-2-EN-1-YL]OXIRAN-2-YL}UNDEC-9-ENOIC ACID
2	IPA	4	Ligand/Ion	ISOPROPYL ALCOHOL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	10Y	3	Ligand/Ion	(9Z)-11-{(2R,3S)-3-[(2Z)-PENT-2-EN-1-YL]OXIRAN-2-YL}UNDEC-9-ENOIC ACID
2	IPA	3	Ligand/Ion	ISOPROPYL ALCOHOL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	10Y	2	Ligand/Ion	(9Z)-11-{(2R,3S)-3-[(2Z)-PENT-2-EN-1-YL]OXIRAN-2-YL}UNDEC-9-ENOIC ACID
2	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:165 , PRO A:166 , SER A:167 , HOH A:470	BINDING SITE FOR RESIDUE PO4 A 201
02	AC2	SOFTWARE	GLU A:18 , PHE A:52 , ASN A:54 , TYR A:90 , TYR A:106 , TYR A:143 , HOH A:409 , HOH A:411	BINDING SITE FOR RESIDUE 10Y A 202
03	AC3	SOFTWARE	TYR A:97 , PRO A:184 , HOH A:446 , HOH A:449	BINDING SITE FOR RESIDUE IPA A 203
04	AC4	SOFTWARE	ASN B:20 , ARG B:22 , ILE B:29 , PHE B:52	BINDING SITE FOR RESIDUE 10Y B 401
05	AC5	SOFTWARE	ASP B:6 , GLN B:12 , HOH B:508	BINDING SITE FOR RESIDUE IPA B 402
06	AC6	SOFTWARE	GLU C:18 , ARG C:22 , PRO C:27 , ILE C:29 , PHE C:52 , ASN C:54 , TYR C:86 , TYR C:90 , TYR C:143 , HOH C:577 , HOH C:594	BINDING SITE FOR RESIDUE 10Y C 401
07	AC7	SOFTWARE	SER D:171 , GLU D:172	BINDING SITE FOR RESIDUE PO4 D 201
08	AC8	SOFTWARE	GLU D:18 , ASN D:20 , ARG D:22 , SER D:26 , PRO D:27 , ASN D:54 , TYR D:90 , TYR D:106 , TYR D:143 , HOH D:374 , HOH D:377	BINDING SITE FOR RESIDUE 10Y D 202
09	AC9	SOFTWARE	GLN D:12 , ILE D:150 , LYS D:152 , HOH D:315 , HOH D:385	BINDING SITE FOR RESIDUE IPA D 203
10	BC1	SOFTWARE	GLU F:18 , ARG F:22 , PRO F:27 , PHE F:52 , ASN F:54 , TYR F:90 , TYR F:106 , TYR F:143 , HOH F:553 , HOH F:559	BINDING SITE FOR RESIDUE 10Y F 401

(no "SS Bond" information available for 4H69)

Asymmetric Unit

No.	Residues
1	Ser A:26	-	Pro A:27
2	Phe A:137	-	Pro A:138
3	Ser B:26	-	Pro B:27
4	Phe B:137	-	Pro B:138
5	Ser C:26	-	Pro C:27
6	Phe C:137	-	Pro C:138
7	Ser D:26	-	Pro D:27
8	Phe D:137	-	Pro D:138
9	Ser E:26	-	Pro E:27
10	Phe E:137	-	Pro E:138
11	Ser F:26	-	Pro F:27
12	Phe F:137	-	Pro F:138

(no "SAP(SNP)/Variant" information available for 4H69)

(no "PROSITE Motif" information available for 4H69)

(no "Exon" information available for 4H69)

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:190
                                                                                                                                                                                                                              
               SCOP domains d4h69a_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheeeeeeeee..........................eeee..eeee.....eeeeeeeeeeeee........eeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h69 A  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVILPFGGENGAHANSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
                                                                 34|                                                                                                                                                      
                                                                  38

Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains d4h69b_ B: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeeeeee................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h69 B  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVIANSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25   ||   48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
                                                            29|                                                                                                                                                 
                                                             43

Chain C from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains d4h69c_ C: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeeeeee................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h69 C  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVILNSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25    ||  48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
                                                             30|                                                                                                                                                
                                                              44

Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains d4h69d_ D: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeeeeee................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h69 D  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVILPSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25     || 48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
                                                              31|                                                                                                                                               
                                                               45

Chain E from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4h69e_ E: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeeeeeee...............ee.....ee.....eeee..eeee.....eeeeeeeeeeeee........eeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h69 E  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVILPFGGKKDENGAHANSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain F from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains d4h69f_ F: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeeeeee....................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee.hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeeeee...eeeeeeeee.....hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h69 F  -4 GPLGSMGNKVDKLAGVQELSVYEINERDRGSPVILPFGANSLGDLVPFSNKVYDGSLQRRLGITAGICTLISHNAEKKGDRYEAQYSFYFGDYGHISVQGPYITYEDTELVVTGGTGIFAGCHGVAKLHQIIFPVKLFYTFYLQGIKKLPEELCASVVPPSPSAEPSEQAKKCHPSSVAPNFTN 188
                                     5        15        25       |44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                                                                33|                                                                                                                                                 
                                                                 43

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: automated matches (2)

Protein domain: automated matches (2)

Physcomitrella patens [TaxId: 145481] (2)

1a	d4h69a_	A:
1b	d4h69e_	E:
1c	d4h69f_	F:
1d	d4h69b_	B:
1e	d4h69c_	C:
1f	d4h69d_	D:

(no "CATH Domain" information available for 4H69)

(no "Pfam Domain" information available for 4H69)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:137 - Pro A:138	[ RasMol ]
		Phe B:137 - Pro B:138	[ RasMol ]
		Phe C:137 - Pro C:138	[ RasMol ]
		Phe D:137 - Pro D:138	[ RasMol ]
		Phe E:137 - Pro E:138	[ RasMol ]
		Phe F:137 - Pro F:138	[ RasMol ]
		Ser A:26 - Pro A:27	[ RasMol ]
		Ser B:26 - Pro B:27	[ RasMol ]
		Ser C:26 - Pro C:27	[ RasMol ]
		Ser D:26 - Pro D:27	[ RasMol ]
		Ser E:26 - Pro E:27	[ RasMol ]
		Ser F:26 - Pro F:27	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	4h69
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(no "Entries Sharing at Least One Protein Chain" available for 4H69)

Description

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Ligands, Modified Residues, Ions (3, 11)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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