2E8U - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM AND IPP (P21)

Authors :   R. T. Guo, C. K. -M. Chen, T. P. Ko, W. Y. Jeng, T. H. Chang, P. H. Liang, E. Oldfield, A. H. -J. Wang

Date :   23 Jan 07 (Deposition) - 12 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

Chains :   Asym./Biol. Unit : A,B

Keywords :   Prenyltransferase, Farnesyl Pyrophosphate, Bisphosphonate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. T. Guo, R. Cao, P. H. Liang, T. P. Ko, T. H. Chang, M. P. Hudock, W. Y. Jeng, C. K. -M. Chen, Y. Zhang, Y. Song, C. J. Kuo, F. Yin, E. Oldfield, A. H. -J. Wang
Bisphosphonates Target Multiple Sites In Both Cis- And Trans-Prenyltransferases
Proc. Natl. Acad. Sci. Usa V. 104 10022 2007
PubMed-ID: 17535895 | Reference-DOI: 10.1073/PNAS.0702254104
(for further references see the PDB file header)

Molecule 1 - GERANYLGERANYL PYROPHOSPHATE SYNTHETASE
	Chains	:	A, B
	EC Number	:	2.5.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET32/LIC
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GGPP SYNTHETASE, GGPPSASE, GERANYLGERANYL DIPHOSPHATE SYNTHASE, BET2 SUPPRESSOR PROTEIN 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	IPE	4	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:80 , ASP A:84 , HOH A:612 , HOH A:763 , IPE A:1102 , MG A:1302	BINDING SITE FOR RESIDUE MG A 1301
2	AC2	SOFTWARE	ASP A:80 , ASP A:84 , HOH A:564 , HOH A:569 , HOH A:765 , IPE A:1102 , MG A:1301	BINDING SITE FOR RESIDUE MG A 1302
3	AC3	SOFTWARE	ASP B:80 , ASP B:84 , HOH B:692 , HOH B:788 , IPE B:1104 , MG B:1304	BINDING SITE FOR RESIDUE MG B 1303
4	AC4	SOFTWARE	ASP B:80 , ASP B:84 , HOH B:558 , HOH B:589 , HOH B:768 , IPE B:1104 , MG B:1303	BINDING SITE FOR RESIDUE MG B 1304
5	AC5	SOFTWARE	LYS A:38 , HIS A:73 , ARG A:90 , TYR A:210 , GLN A:211 , HOH A:601 , HOH A:731 , HOH A:733 , IPE A:1102	BINDING SITE FOR RESIDUE IPE A 1101
6	AC6	SOFTWARE	SER A:76 , ASP A:80 , ASP A:84 , ARG A:89 , LEU A:143 , LYS A:174 , GLN A:211 , ASP A:214 , LYS A:238 , HOH A:569 , HOH A:612 , HOH A:763 , HOH A:765 , IPE A:1101 , MG A:1301 , MG A:1302	BINDING SITE FOR RESIDUE IPE A 1102
7	AC7	SOFTWARE	GLY B:40 , LYS B:41 , ARG B:44 , HIS B:73 , ARG B:90 , TYR B:210 , GLN B:211 , HOH B:543 , HOH B:545 , HOH B:632 , HOH B:636 , IPE B:1104	BINDING SITE FOR RESIDUE IPE B 1103
8	AC8	SOFTWARE	LEU B:77 , ASP B:80 , ASP B:84 , ARG B:89 , LEU B:143 , LYS B:174 , GLN B:211 , ASP B:214 , LYS B:238 , HOH B:548 , HOH B:589 , HOH B:692 , HOH B:767 , HOH B:768 , HOH B:788 , IPE B:1103 , MG B:1303 , MG B:1304	BINDING SITE FOR RESIDUE IPE B 1104

(no "SS Bond" information available for 2E8U)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:157	-	Pro A:158
2	Leu B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 2E8U)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	GGPPS_YEAST	72-86	2	A:77-91 B:77-91
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	GGPPS_YEAST	201-213	2	A:206-218 B:206-218

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPL069C	1	YPL069C.1	XVI:423889-422882	1008	GGPPS_YEAST	1-335	335	2	A:6-305 (gaps) B:9-338 (gaps)	300 330

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:288
 aligned with GGPPS_YEAST | Q12051 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:302
                              1                                                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  
          GGPPS_YEAST     - --MEAKIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLVPFINLLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIK 300
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY--------------------------------------------------------------------------------------- PROSITE
               Transcript 1 --Exon 1.1  PDB: A:6-305 (gaps) UniProt: 1-335 [INCOMPLETE]                                                                                                                                                                                                                                                    Transcript 1
                 2e8u A   4 NKMEAKIDELINNDPVWSSQNESLISKPYNHILLK------LNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPS----HSLVPFINLLGIIYQIRDDYLNLKDFQMS----FAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIK 305
                                    13        23        33    |    - |      53        63        73        83        93       103       113       123       133       143       153       163       173       183        |-   |   203       213       223 |    |233       243       253       263       273       283       293       303  
                                                             38     45                                                                                                                                                192  197                         225  230

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with GGPPS_YEAST | Q12051 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:330
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
          GGPPS_YEAST     4 KIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLVPFINLLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIKNDNENKYLPDLASHSDTATNLHDELLYIIDHLS 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...---..hhhhhhhhhhhhhhhhhhhhhhh..------.hhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.--------------------hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-338 (gaps) UniProt: 1-335 [INCOMPLETE]                                                                                                                                                                                                                                                                                  Transcript 1
                 2e8u B   9 KIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSS---HSLVPFINLLGIIYQIRDDYLNLKDFQ------FAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIKND--------------------DELLYIIDHLS 338
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    |  198       208       218    |    - |     238       248       258       268       278       288       298        |-         -       328       338
                                                                                                                                                                                                                  193 197                       223    230                                                                          307                  328

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 2E8U)

(no "CATH Domain" information available for 2E8U)

(no "Pfam Domain" information available for 2E8U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GGPPS_YEAST | Q12051)

molecular function
	GO:0004161	dimethylallyltranstransferase activity	Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
	GO:0004311	farnesyltranstransferase activity	Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate.
	GO:0004337	geranyltranstransferase activity	Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016117	carotenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
	GO:0045337	farnesyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of farnesyl diphosphate.
	GO:0033384	geranyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of geranyl diphosphate.
	GO:0033386	geranylgeranyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of geranylgeranyl diphosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		IPE	[ 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
		Leu A:157 - Pro A:158	[ RasMol ]
		Leu B:157 - Pro B:158	[ 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
	2e8u
		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
	GGPPS_YEAST \| Q12051
		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)
	2.5.1.30
		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
	GGPPS_YEAST \| Q12051
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2dh4	NATIVE PROTEIN WITHOUT LIGAND
2e8t	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, FSPP AND IPP
2e8v	THE SAME PROTEIN IN COMPLEX WITH PRODUCT GGPP (IN SPACE GROUP, P21)
2e8w	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND IPP
2e8x	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND GPP
2e90	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, PYROPHOSPHATE AND FPP
2e91	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-91
2e92	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH- 261(MINODRONATE)
2e93	THE SAME PROTEIN IN COMPLEX WITH BPH-629
2e94	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-364
2e95	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-675
2e96	THE SAME PROTEIN IN COMPLEX WITH BPH-715
2e97	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM, IPP AND BPH-715

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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