1X06 - JenaLib

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Title :   CRYSTAL STRUCTURE OF UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MG, IPP AND FSPP

Authors :   R. -T. Guo, T. -P. Ko, A. P. -C. Chen, C. -J. Kuo, A. H. -J. Wang, P. -H. Liang

Date :   15 Mar 05 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Enzyme-Substrate Complex, Metal Coordination, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. T. Guo, T. P. Ko, A. P. Chen, C. J. Kuo, A. H. Wang, P. H. Liang
Crystal Structures Of Undecaprenyl Pyrophosphate Synthase In Complex With Magnesium, Isopentenyl Pyrophosphate, And Farnesyl Thiopyrophosphate: Roles Of The Metal Ion And Conserved Residues In Catalysis.
J. Biol. Chem. V. 280 20762 2005
PubMed-ID: 15788389 | Reference-DOI: 10.1074/JBC.M502121200
(for further references see the PDB file header)

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
	Chains	:	A
	EC Number	:	2.5.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET32
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	UPP SYNTHETASE, DI-TRANS,POLY-CIS- DECAPRENYLCISTRANSFERASE, UNDECAPRENYL DIPHOSPHATE SYNTHASE, UDS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	FPS	2	Ligand/Ion	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL]TRIHYDROGEN THIODIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	FPS	4	Ligand/Ion	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL]TRIHYDROGEN THIODIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:194 , ARG A:200 , SER A:202 , HOH A:687 , HOH A:688 , HOH A:731 , HOH A:806 , HOH A:831 , HOH A:832	BINDING SITE FOR RESIDUE PO4 A 903
2	AC2	SOFTWARE	ASP A:26 , HOH A:831 , HOH A:832 , HOH A:833 , FPS A:901	BINDING SITE FOR RESIDUE MG A 900
3	AC3	SOFTWARE	MET A:25 , ASP A:26 , GLY A:27 , ASN A:28 , GLY A:29 , ARG A:30 , ARG A:39 , HIS A:43 , VAL A:50 , ALA A:69 , ASN A:74 , ARG A:77 , TRP A:221 , HOH A:804 , HOH A:831 , HOH A:832 , HOH A:833 , MG A:900	BINDING SITE FOR RESIDUE FPS A 901
4	AC4	SOFTWARE	VAL A:50 , LEU A:93 , GLU A:96 , HOH A:812	BINDING SITE FOR RESIDUE FPS A 902

(no "SS Bond" information available for 1X06)

(no "Cis Peptide Bond" information available for 1X06)

(no "SAP(SNP)/Variant" information available for 1X06)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPP_SYNTHASE	PS01066	Undecaprenyl pyrophosphate synthase family signature.	UPPS_ECOLI	190-207	1	A:190-207

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPP_SYNTHASE	PS01066	Undecaprenyl pyrophosphate synthase family signature.	UPPS_ECOLI	190-207	2	A:190-207

(no "Exon" information available for 1X06)

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:229
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:229
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
           UPPS_ECOLI    12 KLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d1x06a_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 1x06A00 A:12-240  [code=3.40.1180.10, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------Prenyltransf-1x06A01 A:24-240                                                                                                                                                                                             Pfam domains
         Sec.struct. author ..hhhhh.eeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee..................eeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x06 A  12 KLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Undecaprenyl diphosphate synthase (32)

Superfamily: Undecaprenyl diphosphate synthase (32)

Family: Undecaprenyl diphosphate synthase (26)

Protein domain: automated matches (11)

Escherichia coli [TaxId: 562] (9)

d1x06a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Undecaprenyl pyrophosphate synthetase (15)

Homologous Superfamily: [code=3.40.1180.10, no name defined] (15)

Escherichia coli. Organism_taxid: 562. (11)

1x06A00

A:12-240

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

)

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

Family: Prenyltransf (8)

Escherichia coli (strain K12) (5)

Prenyltransf-1x06A01

A:24-240

Asymmetric Unit(hide GO term definitions)

Chain A (UPPS_ECOLI | P60472)

molecular function
	GO:0008834	di-trans,poly-cis-decaprenylcistransferase activity	Catalysis of the reaction: di-trans-poly-cis-decaprenyl diphosphate + isopentenyl diphosphate = diphosphate + di-trans-poly-cis-undecaprenyl 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).
biological process
	GO:0043164	Gram-negative-bacterium-type cell wall biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Gram-negative bacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	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.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
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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	1x06
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1jp3	APO ENZYME
1ueh	COMPLEX WITH TRITON, MG AND SO4
1v7u	COMPLEX WITH FPP
1x07	COMPLEX WITH MG AND ISOPENTENYL PYROPHOSPHATE
1x08	D26A MUTANT COMPLEX WITH MG, ISOPENTENYL PYROPHOSPHATE AND FARNESYL THIOPYROPHOSPHATE
1x09	D26A MUTANT COMPLEX WITH MG, ISOPENTENYL PYROPHOSPHATE

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