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Asym./Biol. Unit (Jmol Viewer)

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Title :   E. COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-676

Authors :   R. T. Guo, R. Cao, T. P. Ko, P. H. Liang, E. Oldfield, A. H. J. Wang

Date :   24 Jan 07 (Deposition) - 12 Jun 07 (Release) - 17 Jun 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Cell Wall, Prenyltransferase, Farnesyl Pyrophosphate, Bisphosphonate, Antibiotic (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 - UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
	Chains	:	A, B
	EC Number	:	2.5.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32/LIC
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	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	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	B76	3	Ligand/Ion	[1-HYDROXY-2-(1,1':3',1''-TERPHENYL-3-YLOXY)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:28 , HIS A:43 , PHE A:70 , SER A:71 , HOH A:486	BINDING SITE FOR RESIDUE B76 A 701
2	AC2	SOFTWARE	VAL A:50 , VAL A:54 , SER A:55 , ASN A:59 , GLU A:96 , SER A:99 , LEU A:100 , HIS A:103 , LEU A:139 , ILE A:141	BINDING SITE FOR RESIDUE B76 A 702
3	AC3	SOFTWARE	VAL B:50 , VAL B:54 , ASN B:59 , GLU B:96 , LEU B:100 , HIS B:103 , HOH B:485	BINDING SITE FOR RESIDUE B76 B 703

(no "SS Bond" information available for 2E9D)

(no "Cis Peptide Bond" information available for 2E9D)

(no "SAP(SNP)/Variant" information available for 2E9D)

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.	UPPS_ECOLI	190-207	2	A:190-207 B:190-207

(no "Exon" information available for 2E9D)

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:218
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:225
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
           UPPS_ECOLI    16 HGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d2e9da_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 2e9dA00 A:16-240  [code=3.40.1180.10, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee..-------hhhhhhhhhhhhhhh.hhhhhhhh...eee........hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e9d A  16 HGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS-------AQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    25        35        45        55        65     |   -   |    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
                                                                                  71      79

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:227
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
           UPPS_ECOLI    17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRF 243
               SCOP domains d2e9db_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 2e9dB00 B:17-243  [code=3.40.1180.10, no name defined]                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee...----------hhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e9d B  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSS----------SALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRF 243
                                    26        36        46        56        66     |   -      | 86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
                                                                                  72         83

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(

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Folds(

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Superfamilies( (-)

)

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)

1a	d2e9da_	A:
1b	d2e9db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

1a	2e9dA00	A:16-240
1b	2e9dB00	B:17-243

(no "Pfam Domain" information available for 2E9D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		B76	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e9d)

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	2e9d
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	UPPS_ECOLI \| P60472
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	2.5.1.31
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1x06	WILD-TYPE UPPS IN COMPLEX WITH MG, FSPP AND IPP
1x07	WILD-TYPE UPPS IN COMPLEX WITH MG AND IPP
1x08	D26A MUTANT UPPS IN COMPLEX WITH MG, FSPP AND IPP
1x09	D26A MUTANT UPPS IN COMPLEX WITH MG AND IPP
2e98	THE SAME PROTEIN COMPLEX WITH BPH-629
2e99	THE SAME PROTEIN COMPLEX WITH BPH-608
2e9a	THE SAME PROTEIN COMPLEX WITH BPH-628
2e9c	THE SAME PROTEIN COMPLEX WITH BPH-675

Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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