1RQJ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   ACTIVE CONFORMATION OF FARNESYL PYROPHOSPHATE SYNTHASE BOUND TO ISOPENTYL PYROPHOSPHATE AND RISEDRONATE

Authors :   D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanso

Date :   05 Dec 03 (Deposition) - 02 Mar 04 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Bisphosphonate, Isoprenyl Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanson, J. Finn
Structural Basis For Bisphosphonate-Mediated Inhibition Of Isoprenoid Biosynthesis
J. Biol. Chem. V. 279 8526 2004
PubMed-ID: 14672944 | Reference-DOI: 10.1074/JBC.C300511200

Molecule 1 - GERANYLTRANSTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.5.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ISPA, B0421
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	FARNESYL-DIPHOSPHATE SYNTHASE, FPP SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	IPE	2	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION
3	RIS	2	Ligand/Ion	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	RIS	1	Ligand/Ion	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	RIS	1	Ligand/Ion	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	RIS	1	Ligand/Ion	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP B:244 , ASP B:248 , RIS B:903 , HOH B:933 , HOH B:999 , HOH B:1000	BINDING SITE FOR RESIDUE MG B 904
02	AC2	SOFTWARE	ASP B:105 , ASP B:111 , RIS B:903 , MG B:906 , HOH B:913 , HOH B:1002 , HOH B:1003	BINDING SITE FOR RESIDUE MG B 905
03	AC3	SOFTWARE	ASP B:105 , ASP B:111 , RIS B:903 , MG B:905 , HOH B:945 , HOH B:1001	BINDING SITE FOR RESIDUE MG B 906
04	AC4	SOFTWARE	ASP A:105 , ASP A:111 , RIS A:901 , MG A:909 , HOH A:933 , HOH A:945	BINDING SITE FOR RESIDUE MG A 907
05	AC5	SOFTWARE	ASP A:244 , RIS A:901 , HOH A:918 , HOH A:1031 , HOH A:1032	BINDING SITE FOR RESIDUE MG A 908
06	AC6	SOFTWARE	ASP A:105 , ASP A:111 , RIS A:901 , MG A:907 , HOH A:922 , HOH A:926 , HOH A:1034	BINDING SITE FOR RESIDUE MG A 909
07	AC7	SOFTWARE	GLY A:65 , LYS A:66 , ARG A:69 , HIS A:98 , ARG A:117 , THR A:203 , PHE A:240 , GLN A:241 , RIS A:901 , HOH A:912 , HOH A:913 , HOH A:917 , HOH A:919 , HOH A:973 , HOH A:997	BINDING SITE FOR RESIDUE IPE A 900
08	AC8	SOFTWARE	ASP A:105 , ASP A:111 , ARG A:116 , GLN A:179 , LYS A:202 , THR A:203 , GLN A:241 , ASP A:244 , LYS A:258 , IPE A:900 , MG A:907 , MG A:908 , MG A:909 , HOH A:918 , HOH A:922 , HOH A:933 , HOH A:945 , HOH A:1031 , HOH A:1032 , HOH A:1033 , HOH A:1034	BINDING SITE FOR RESIDUE RIS A 901
09	AC9	SOFTWARE	GLY B:65 , LYS B:66 , ARG B:69 , HIS B:98 , ARG B:117 , THR B:203 , PHE B:240 , GLN B:241 , RIS B:903 , HOH B:909 , HOH B:910 , HOH B:911 , HOH B:916 , HOH B:918 , HOH B:960	BINDING SITE FOR RESIDUE IPE B 902
10	BC1	SOFTWARE	ASP B:105 , ASP B:111 , ARG B:116 , GLN B:179 , LYS B:202 , THR B:203 , ASP B:244 , LYS B:258 , IPE B:902 , MG B:904 , MG B:905 , MG B:906 , HOH B:913 , HOH B:927 , HOH B:933 , HOH B:945 , HOH B:983 , HOH B:999 , HOH B:1000 , HOH B:1001 , HOH B:1002	BINDING SITE FOR RESIDUE RIS B 903

(no "SS Bond" information available for 1RQJ)

(no "Cis Peptide Bond" information available for 1RQJ)

(no "SAP(SNP)/Variant" information available for 1RQJ)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	ISPA_ECOLI	81-97	2	A:102-118 B:102-118
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	ISPA_ECOLI	215-227	2	A:236-248 B:236-248

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	ISPA_ECOLI	81-97	1	A:102-118 -
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	ISPA_ECOLI	215-227	1	A:236-248 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	ISPA_ECOLI	81-97	1	- B:102-118
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	ISPA_ECOLI	215-227	1	- B:236-248

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	ISPA_ECOLI	81-97	2	A:102-118 B:102-118
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	ISPA_ECOLI	215-227	2	A:236-248 B:236-248

(no "Exon" information available for 1RQJ)

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:299
 aligned with ISPA_ECOLI | P22939 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
           ISPA_ECOLI     1 MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 299
               SCOP domains d1rqja_ A: Farnesyl diphosphate synthase (geranyltranstransferase)                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1rqjA00 A:22-320 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------POLYPRENYL_SYNTHA---------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqj A  22 MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 320
                                    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

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with ISPA_ECOLI | P22939 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:298
                                    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        
           ISPA_ECOLI     2 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 299
               SCOP domains d1rqjb_ B: Farnesyl diphosphate synthase (geranyltranstransferase)                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1rqjB00 B:23-320 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------polyprenyl_synt-1rqjB01 B:53-316                                                                                                                                                                                                                                        ---- Pfam domains (1)
           Pfam domains (2) ------------------------------polyprenyl_synt-1rqjB02 B:53-316                                                                                                                                                                                                                                        ---- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------POLYPRENYL_SYNTHA---------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqj B  23 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 320
                                    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

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: Isoprenyl diphosphate synthases (57)

Protein domain: Farnesyl diphosphate synthase (geranyltranstransferase) (8)

Escherichia coli [TaxId: 562] (2)

1a	d1rqja_	A:
1b	d1rqjb_	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)

Escherichia coli. Organism_taxid: 562. (2)

1a	1rqjA00	A:22-320
1b	1rqjB00	B:23-320

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: polyprenyl_synt (86)

Escherichia coli (strain K12) (2)

1a	polyprenyl_synt-1rqjB01	B:53-316
1b	polyprenyl_synt-1rqjB02	B:53-316

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISPA_ECOLI | P22939)

molecular function
	GO:0004161	dimethylallyltranstransferase activity	Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl 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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rqj)

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	1rqj
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Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

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