2VG0 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RV1086 CITRONELLY PYROPHOSPHATE COMPLEX

Authors :   J. H. Naismith, W. Wang, C. Dong

Date :   07 Nov 07 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Peptidoglycan Synthesis, Cell Wall Biogenesis/Degradation, Secreted, Cell Shape, Transferase, Prenyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Wang, C. Dong, M. Mcneil, D. Kaur, S. Mahapatra, D. C. Crick, J. H. Naismith
The Structural Basis Of Chain Length Control In Rv1086
J. Mol. Biol. V. 381 129 2008
PubMed-ID: 18597781 | Reference-DOI: 10.1016/J.JMB.2008.05.060

Molecule 1 - SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE
	Chains	:	A, B
	EC Number	:	2.5.1.68
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL12 DE3
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 30-256
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	RV1086, Z-FPP SYNTHETASE, Z-ISOPRENYL DIPHOSPHATE SYNTHASE, Z-FPPS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	GPP	2	Ligand/Ion	GERANYL DIPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:39 , ASP A:40 , GLY A:41 , ASN A:42 , ARG A:43 , ARG A:44 , TYR A:58 , GLY A:61 , ALA A:62 , ILE A:65 , LEU A:84 , ASN A:89 , ARG A:92 , HOH A:2222	BINDING SITE FOR RESIDUE GPP A1257
2	AC2	SOFTWARE	CYS B:39 , ASP B:40 , GLY B:41 , ASN B:42 , ARG B:43 , ARG B:44 , TYR B:58 , GLY B:61 , LEU B:84 , ASN B:89 , ARG B:92 , HOH B:2256	BINDING SITE FOR RESIDUE GPP B1257
3	AC3	SOFTWARE	GLU A:163 , ASP A:166 , ALA A:167 , ASN A:197 , LEU A:198 , TYR A:199 , HOH A:2223	BINDING SITE FOR RESIDUE GOL A1258
4	AC4	SOFTWARE	GLU B:163 , ASP B:166 , ALA B:167 , ALA B:170 , ASN B:197 , LEU B:198 , TYR B:199 , HOH B:2257	BINDING SITE FOR RESIDUE GOL B1258
5	AC5	SOFTWARE	ARG A:70 , ARG B:242 , HIS B:243 , VAL B:244 , HOH B:2258 , HOH B:2259 , HOH B:2260	BINDING SITE FOR RESIDUE GOL B1259

(no "SS Bond" information available for 2VG0)

(no "Cis Peptide Bond" information available for 2VG0)

(no "SAP(SNP)/Variant" information available for 2VG0)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPP_SYNTHASE	PS01066	Undecaprenyl pyrophosphate synthase family signature.	ZFPP_MYCTO	207-224	2	A:207-224 B:207-224
1	UPP_SYNTHASE	PS01066	Undecaprenyl pyrophosphate synthase family signature.	ZFPP_MYCTU	207-224	2	A:207-224 B:207-224

(no "Exon" information available for 2VG0)

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:227
 aligned with ZFPP_MYCTO | P9WFF4 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           ZFPP_MYCTO    30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
               SCOP domains d2vg0a_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vg0 A  30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain A from PDB  Type:PROTEIN  Length:227
 aligned with ZFPP_MYCTU | P9WFF5 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           ZFPP_MYCTU    30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
               SCOP domains d2vg0a_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vg0 A  30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ZFPP_MYCTO | P9WFF4 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           ZFPP_MYCTO    30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
               SCOP domains d2vg0b_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Prenyltransf-2vg0B01 B:38-256                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) --------Prenyltransf-2vg0B02 B:38-256                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ....eeeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vg0 B  30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ZFPP_MYCTU | P9WFF5 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:227
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           ZFPP_MYCTU    30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
               SCOP domains d2vg0b_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Prenyltransf-2vg0B01 B:38-256                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) --------Prenyltransf-2vg0B02 B:38-256                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ....eeeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vg0 B  30 DLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Undecaprenyl diphosphate synthase (32)

Superfamily: Undecaprenyl diphosphate synthase (32)

Family: automated matches (6)

Protein domain: automated matches (6)

Mycobacterium tuberculosis [TaxId: 1773] (3)

1a	d2vg0a_	A:
1b	d2vg0b_	B:

(no "CATH Domain" information available for 2VG0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Prenyltransf] (8)

Family: Prenyltransf (8)

Mycobacterium tuberculosis (3)

1a	Prenyltransf-2vg0B01	B:38-256
1b	Prenyltransf-2vg0B02	B:38-256

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ZFPP_MYCTU | P9WFF5)

molecular function
	GO:0033850	Z-farnesyl diphosphate synthase activity	Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-cis,6-trans-farnesyl diphosphate + diphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	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.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
	GO:0016094	polyprenol biosynthetic process	The chemical reactions and pathways resulting in the formation of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans.
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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (ZFPP_MYCTO | P9WFF4)

molecular function
	GO:0033850	Z-farnesyl diphosphate synthase activity	Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-cis,6-trans-farnesyl diphosphate + diphosphate.
	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:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	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.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vg0)

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	2vg0
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	ZFPP_MYCTO \| P9WFF4
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		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	ZFPP_MYCTU \| P9WFF5
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	2.5.1.68
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		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	ZFPP_MYCTO \| P9WFF4
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	ZFPP_MYCTU \| P9WFF5
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UniProtKB/Swiss-Prot
	ZFPP_MYCTO \| P9WFF4	:	2vfw 2vg1
	ZFPP_MYCTU \| P9WFF5	:	2vfw 2vg1

2vfw	RV1086 NATIVE
2vg1	RV1086 E,E-FARNESYL DIPHOSPHATE COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (12, 21)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File