3P5P - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF TAXADIENE SYNTHASE FROM PACIFIC YEW (TAXUS BREVIFOLIA) IN COMPLEX WITH MG2+ AND 13-AZA-13,14-DIHYDROCOPALYL DIPHOSPHATE

Authors :   M. Koksal, D. W. Christianson

Date :   10 Oct 10 (Deposition) - 29 Dec 10 (Release) - 19 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

Chains :   Asym./Biol. Unit : A

Keywords :   Class I And Ii Terpene Cyclase Fold, Diterpene Cyclase, Ddxxd Motif, Nse/Dte Motif, 3-Azacopalyl Diphosphate, Biosynthesis Of Paclitaxel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Koksal, Y. Jin, R. M. Coates, R. Croteau, D. W. Christianson
Taxadiene Synthase Structure And Evolution Of Modular Architecture In Terpene Biosynthesis.
Nature V. 469 116 2011
PubMed-ID: 21160477 | Reference-DOI: 10.1038/NATURE09628

Molecule 1 - TAXADIENE SYNTHASE
	Chains	:	A
	EC Number	:	4.2.3.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22BTV
	Expression System Strain	:	BL21(DE3) CODONPLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 108-862
	Gene	:	TDC1
	Organism Common	:	PACIFIC YEW
	Organism Scientific	:	TAXUS BREVIFOLIA
	Organism Taxid	:	46220
	Synonym	:	TAXA-4(5),11(12)-DIENE SYNTHASE
	Tissue	:	STEM

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	A3C	2	Ligand/Ion	2-(METHYL{2-[(1S,4AS,8AS)-5,5,8A-TRIMETHYL-2-METHYLIDENEDECAHYDRONAPHTHALEN-1-YL]ETHYL}AMINO)ETHYLTRIHYDROGEN DIPHOSPHATE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , ASN A:757 , THR A:761 , GLU A:765 , A3C A:911	BINDING SITE FOR RESIDUE MG A 901
2	AC2	SOFTWARE	HOH A:2 , HOH A:4 , HOH A:6 , HOH A:10 , ASP A:617 , A3C A:911 , HOH A:936	BINDING SITE FOR RESIDUE MG A 902
3	AC3	SOFTWARE	HOH A:887 , HOH A:1254 , HOH A:1302 , HOH A:1366 , HOH A:1611	BINDING SITE FOR RESIDUE MG A 903
4	AC4	SOFTWARE	HOH A:1 , HOH A:2 , HOH A:3 , HOH A:4 , HOH A:5 , HOH A:8 , HOH A:9 , HOH A:11 , SER A:587 , GLY A:606 , VAL A:714 , ARG A:754 , ASN A:757 , THR A:761 , GLU A:765 , TYR A:835 , MG A:901 , MG A:902 , HOH A:1511	BINDING SITE FOR RESIDUE A3C A 911
5	AC5	SOFTWARE	ARG A:580 , TYR A:835 , HOH A:1475	BINDING SITE FOR RESIDUE A3C A 912
6	AC6	SOFTWARE	HOH A:24 , MET A:414 , TRP A:502 , TYR A:809 , ASN A:826 , HOH A:1027 , HOH A:1214	BINDING SITE FOR RESIDUE EDO A 921
7	AC7	SOFTWARE	HOH A:15 , SER A:357 , ASN A:403 , LEU A:407 , ARG A:446 , ASN A:450 , TRP A:524 , HOH A:996	BINDING SITE FOR RESIDUE EDO A 922
8	AC8	SOFTWARE	HOH A:88 , TRP A:386 , GLU A:388 , SER A:420	BINDING SITE FOR RESIDUE EDO A 923

(no "SS Bond" information available for 3P5P)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:348	-	Ser A:349
2	Tyr A:741	-	Pro A:742

(no "SAP(SNP)/Variant" information available for 3P5P)

(no "PROSITE Motif" information available for 3P5P)

(no "Exon" information available for 3P5P)

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:745
 aligned with TASY_TAXBR | Q41594 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:752
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860  
           TASY_TAXBR   111 TYQERADELVVKIKDMFNALGDGDISPSAYDTAWVARLATISSDGSEKPRFPQALNWVFNNQLQDGSWGIESHFSLCDRLLNTTNSVIALSVWKTGHSQVQQGAEFIAENLRLLNEEDELSPDFQIIFPALLQKAKALGINLPYDLPFIKYLSTTREARLTDVSAAADNIPANMLNALEGLEEVIDWNKIMRFQSKDGSFLSSPASTACVLMNTGDEKCFTFLNNLLDKFGGCVPCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLVPDLNTTALGLRTLRMHGYNVSSDVLNNFKDENGRFFSSAGQTHVELRSVVNLFRASDLAFPDERAMDDARKFAEPYLREALATKISTNTKLFKEIEYVVEYPWHMSIPRLEARSYIDSYDDNYVWQRKTLYRMPSLSNSKCLELAKLDFNIVQSLHQEELKLLTRWWKESGMADINFTRHRVAEVYFSSATFEPEYSATRIAFTKIGCLQVLFDDMADIFATLDELKSFTEGVKRWDTSLLHEIPECMQTCFKVWFKLMEEVNNDVVKVQGRDMLAHIRKPWELYFNCYVQEREWLEAGYIPTFEEYLKTYAISVGLGPCTLQPILLMGELVKDDVVEKVHYPSNMFELVSLSWRLTNDTKTYQAEKARGQQASGIACYMKDNPGATEEDAIKHICRVVDRALKEASFEYFKPSNDIPMGCKSFIFNLRLCVQIFYKFIDGYGIANEEIKDYIRKVYIDPIQV 862
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Terpene_synth-3p5pA01 A:297-498                                                                                                                                                                           -----------------------------------------Terpene_synth_C-3p5pA02 A:540-806                                                                                                                                                                                                                                          -------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhheee.....eee.hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh....hhhhhhhhh...............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..-------..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p5p A 111 TYQERADELVVKIKDMFNALGDGDISPSAYDTAWVARLATISSDGSEKPRFPQALNWVFNNQLQDGSWGIESHFSLCDRLLNTTNSVIALSVWKTGHSQVQQGAEFIAENLRLLNEEDELSPDFQIIFPALLQKAKALGINLPYDLPFIKYLSTTREARLTDVSAAADNIPANMLNALEGLEEVIDWNKIMRFQSKDGSFLSSPASTACVLMNTGDEKCFTFLNNLLDKFGGCVPCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLVPDLNTTALGLRTLRMHGYNVSSDVLNNFKDENGRFFSSAGQTHVELRSVVNLFRASDLAFPDERAMDDARKFAEPYLREALATKISTNTKLFKEIEYVVEYPWHMSIPRLEARSYIDSYDDNYVWQRKTLYRMPSLSNSKCLELAKLDFNIVQSLHQEELKLLTRWWKESGMADINFTRHRVAEVYFSSATFEPEYSATRIAFTKIGCLQVLFDDMADIFATLDELKSFTEGVKRWDTSLLHEIPECMQTCFKVWFKLMEEVNNDVVKVQGRDMLAHIRKPWELYFNCYVQEREWLEAGYIPTFEEYLKTYAISVGLGPCTLQPILLMGELVKDDVVEKVHYPSNMFELVSLSWRLTNDTKTYQAEKARGQQASGIACYMKDNPGATEEDAIKHICRVVDRALKEASFEYFKPSNDIPMGCKSFIFNLRLCVQIFYKF-------NEEIKDYIRKVYIDPIQV 862
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      |  -    |  850       860  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                837     845

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 "SCOP Domain" information available for 3P5P)

(no "CATH Domain" information available for 3P5P)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TASY_TAXBR | Q41594)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0050553	taxadiene synthase activity	Catalysis of the reaction: all-trans-geranylgeranyl diphosphate = diphosphate + taxa-4,11-diene.
	GO:0010333	terpene synthase activity	Catalysis of the formation of cyclic terpenes through the cyclization of linear terpenes (e.g. isopentenyl-PP, geranyl-PP, farnesyl-PP and geranylgeranyl-PP) containing varying numbers of isoprene units.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0042617	paclitaxel biosynthetic process	The chemical reactions and pathways resulting in the formation of paclitaxel, an alkaloid compound used as an anticancer treatment.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		A3C	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:348 - Ser A:349	[ RasMol ]
		Tyr A:741 - Pro A:742	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3p5p
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TASY_TAXBR \| Q41594
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.2.3.17
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TASY_TAXBR \| Q41594
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TASY_TAXBR \| Q41594	:	3p5r

3p5r	THE SAME PROTEIN IN COMPLEX WITH MG2+ AND 2-FLUORO- GERANYLGERANYL DIPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File