2AET - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   R304K TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4S)-7-AZABISABOLENE

Authors :   L. S. Vedula, D. E. Cane, D. W. Christianson

Date :   23 Jul 05 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Pyrophosphate, Terpenoid Synthase Fold, Site-Directed Mutagenesis, (4S)-7-Azabisabolene, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. S. Vedula, D. E. Cane, D. W. Christianson
Role Of Arginine-304 In The Diphosphate-Triggered Active Site Closure Mechanism Of Trichodiene Synthase.
Biochemistry V. 44 12719 2005
PubMed-ID: 16171386 | Reference-DOI: 10.1021/BI0510476

Molecule 1 - TRICHODIENE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.3.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRI5
	Mutation	:	YES
	Organism Scientific	:	FUSARIUM SPOROTRICHIOIDES
	Organism Taxid	:	5514
	Synonym	:	SESQUITERPENE CYCLASE, TS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	-1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:225 , ASP B:226 , SER B:229 , GLU B:233 , POP B:700	BINDING SITE FOR RESIDUE MG B 701
2	AC2	SOFTWARE	ASP B:100 , POP B:700	BINDING SITE FOR RESIDUE MG B 702
3	AC3	SOFTWARE	ASP B:100 , GLU B:164 , ASN B:185 , POP B:700	BINDING SITE FOR RESIDUE MG B 703
4	AC4	SOFTWARE	ASP B:100 , ARG B:182 , ASN B:225 , SER B:229 , LYS B:232 , GLU B:233 , LYS B:304 , TYR B:305 , MG B:701 , MG B:702 , MG B:703	BINDING SITE FOR RESIDUE POP B 700
5	AC5	SOFTWARE	TYR A:113 , TRP A:128 , ASN A:132 , PHE B:114	BINDING SITE FOR RESIDUE EDO A 750
6	AC6	SOFTWARE	PHE A:114 , TYR B:113 , TRP B:128 , ASN B:132 , ILE B:151	BINDING SITE FOR RESIDUE EDO B 751

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

Asymmetric Unit

No.	Residues
1	Tyr A:345	-	Pro A:346
2	Tyr B:345	-	Pro B:346

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

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

(no "Exon" information available for 2AET)

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:352
 aligned with TRI5_FUSSP | P13513 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352  
           TRI5_FUSSP     3 NFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
               SCOP domains d2aeta_ A: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2aetA00 A:3-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aet A   3 NFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRKYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:353
 aligned with TRI5_FUSSP | P13513 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:353
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351   
           TRI5_FUSSP     2 ENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
               SCOP domains d2aetb_ B: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2aetB00 B:2-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aet B   2 ENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRKYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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 alpha proteins (14657)

Fold: Terpenoid synthases (196)

Superfamily: Terpenoid synthases (196)

Family: Trichodiene synthase (20)

Protein domain: Trichodiene synthase (20)

Fusarium sporotrichioides [TaxId: 5514] (20)

1a	d2aeta_	A:
1b	d2aetb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Fusarium sporotrichioides. Organism_taxid: 5514. (20)

1a	2aetA00	A:3-354
1b	2aetB00	B:2-354

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRI5_FUSSP | P13513)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0045482	trichodiene synthase activity	Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = diphosphate + trichodiene.
biological process
	GO:0016106	sesquiterpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:345 - Pro A:346	[ RasMol ]
		Tyr B:345 - Pro B:346	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	2aet
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Access by UniProt ID/Accession number
	TRI5_FUSSP \| P13513
		Comparative Protein Structure Models	:	ModBase
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Access by Enzyme Classificator (EC Number)
	4.2.3.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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Access by UniProt ID/Accession number
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1jfa	TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WITH DIPHOSPHATE
1jfg	TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES
1yys	Y305F TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4S)-7-AZABISABOLENE
1yyu	D100E TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4S)-7-AZABISABOLENE
2aek	R304K TRICHODIENE SYNTHASE
2ael	R304K TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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CATH Domains (1, 2)

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Gene Ontology (3, 3)

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