2Z4X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM AND BPH-252 (P21)

Authors :   R. T. Guo, C. K. -M. Chen, M. Hudock, R. Cao, E. Oldfield, A. H. -J. Wang

Date :   26 Jun 07 (Deposition) - 01 Jul 08 (Release) - 29 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Prenyltransferase, Geranylgeranyl Pyrophosphate, Bisphosphonate, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. -M. Chen, M. P. Hudock, Y. Zhang, R. -T. Guo, R. Cao, J. H. No, P. -H. Liang, T. -P. Ko, T. -H. Chang, S. -C. Chang, Y. Song, J. Axelson, A. Kumar, A. H. -J. Wang, E. Oldfield
Inhibition Of Geranylgeranyl Diphosphate Synthase By Bisphosphonates: A Crystallographic And Computational Investigation
J. Med. Chem. V. 51 5594 2008
PubMed-ID: 18800762 | Reference-DOI: 10.1021/JM800325Y

Molecule 1 - GERANYLGERANYL PYROPHOSPHATE SYNTHETASE
	Chains	:	A, B
	EC Number	:	2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET32 XA/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	252	2	Ligand/Ion	(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
2	MG	6	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:80 , ASP A:84 , HOH A:1214 , HOH A:1224	BINDING SITE FOR RESIDUE MG A 1201
2	AC2	SOFTWARE	ASP A:80 , ASP A:84 , HOH A:1217 , HOH A:1512 , HOH A:1516	BINDING SITE FOR RESIDUE MG A 1202
3	AC3	SOFTWARE	HOH A:1308 , HOH A:1477 , HOH A:1481 , HOH A:1555	BINDING SITE FOR RESIDUE MG A 1203
4	AC4	SOFTWARE	ASP B:80 , ASP B:84 , HOH B:1208 , HOH B:1222	BINDING SITE FOR RESIDUE MG B 1204
5	AC5	SOFTWARE	ASP B:80 , ASP B:84 , HOH B:1239 , HOH B:1336 , HOH B:1338	BINDING SITE FOR RESIDUE MG B 1205
6	AC6	SOFTWARE	ASP B:214 , HOH B:1213 , HOH B:1253	BINDING SITE FOR RESIDUE MG B 1206
7	AC7	SOFTWARE	SER A:76 , ASP A:80 , ASP A:84 , ARG A:89 , LEU A:143 , HIS A:144 , LYS A:174 , LYS A:238 , HOH A:1214 , HOH A:1224 , HOH A:1317 , HOH A:1365 , HOH A:1471 , HOH A:1477 , HOH A:1481 , HOH A:1512 , HOH A:1516 , HOH A:1555	BINDING SITE FOR RESIDUE 252 A 1101
8	AC8	SOFTWARE	ASP B:80 , ASP B:84 , ARG B:89 , LEU B:143 , HIS B:144 , GLN B:147 , LYS B:174 , ASP B:214 , LYS B:238 , HOH B:1208 , HOH B:1213 , HOH B:1222 , HOH B:1238 , HOH B:1239 , HOH B:1253 , HOH B:1336 , HOH B:1404 , HOH B:1435	BINDING SITE FOR RESIDUE 252 B 1102

(no "SS Bond" information available for 2Z4X)

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 2Z4X)

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:9-307 (gaps)	300 299

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:286
 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 hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh--------hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhhhhhhhhhhhhhh----.hhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh 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
                 2z4x A   4 NKMEAKIDELINNDPVWSSQNESLISKPYNHILL--------NLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPS----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  
                                                            37       46                                                                                                                                               192  197                         225  230

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with GGPPS_YEAST | Q12051 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:299
                                    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         
          GGPPS_YEAST     4 KIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLVPFINLLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIKND 302
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------polyprenyl_sy     nt-2z4xB01 B:28-282                                                                                                                                                                                                                          ------------------------- Pfam domains (1)
           Pfam domains (2) -------------------polyprenyl_sy     nt-2z4xB02 B:28-282                                                                                                                                                                                                                          ------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhh.....hhhhhhhhhhhhhhhhh...-----hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...---..hhhhhhhhhhhhhhhhhhhhhhh..------.hhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY----------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-307 (gaps) UniProt: 1-335 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 2z4x B   9 KIDELINNDPVWSSQNESLISKPYNHILLKPG-----NLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSS---HSLVPFINLLGIIYQIRDDYLNLKDFQ------FAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIKND 307
                                    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         
                                                          40    46                                                                                                                                                193 197                       223    230

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 2Z4X)

(no "CATH Domain" information available for 2Z4X)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: polyprenyl_synt] (86)

Family: polyprenyl_synt (86)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (12)

1a	polyprenyl_synt-2z4xB01	B:28-282
1b	polyprenyl_synt-2z4xB02	B:28-282

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

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	Cis Peptide Bonds
		Leu A:157 - Pro A:158	[ RasMol ]
		Leu B:157 - Pro B:158	[ RasMol ]

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	2z4x
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	2.5.1.1
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	2.5.1.10
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	2.5.1.29
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	2.5.1.30
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2z4v	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND GGPP (INHIBITORY SITE)
2z4w	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-749
2z4y	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-252
2z4z	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-SC01
2z50	THE SAME PROTEIN IN COMPLEX WITH BPH-28
2z52	THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND BPH-23

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 (1, 2)

Gene Ontology (14, 14)

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