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Title :   CRYSTAL STRUCTURE OF E. COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-1290

Authors :   R. Cao, Y. -L. Liu, E. Oldfield

Date :   15 Jun 11 (Deposition) - 19 Dec 12 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

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

Keywords :   Alpha/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Zhu, Y. Zhang, W. Sinko, M. E. Hensler, J. Olson, K. J. Molohon, S. Lindert, R. Cao, K. Li, K. Wang, Y. Wang, Y. L. Liu, A. Sankovsky, C. A. De Oliveira, D. A. Mitchell, V. Nizet, J. A. Mccammon, E. Oldfiel
Antibacterial Drug Leads Targeting Isoprenoid Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 110 123 2013
PubMed-ID: 23248302 | Reference-DOI: 10.1073/PNAS.1219899110

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
	Chains	:	B, A
	EC Number	:	2.5.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	B0174, ISPU, JW0169, RTH, UPPS, YAES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	UPP SYNTHASE, 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, 5)

No.	Name	Count	Type	Full Name
1	2BJ	5	Ligand/Ion	2-{[3-(3,4-DIMETHYLPHENOXY)PHENYL]CARBAMOYL}-4-NITROBENZOIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:24 , MET A:25 , ASP A:26 , GLY A:27 , ASN A:28 , GLY A:29 , ARG A:39 , HIS A:43 , TYR A:68 , ALA A:69 , PHE A:70 , SER A:71 , GLU A:73 , ASN A:74 , ARG A:194 , HOH A:286 , HOH A:342 , 2BJ A:3001 , 2BJ A:4001	BINDING SITE FOR RESIDUE 2BJ A 2001
2	AC2	SOFTWARE	MET A:25 , LEU A:67 , ALA A:69 , PHE A:70 , TRP A:75 , MET A:86 , PHE A:89 , GLU A:96 , PHE A:116 , ILE A:141 , ALA A:142 , ALA A:143 , ASN A:144 , HOH A:266 , HOH A:274 , HOH A:368 , 2BJ A:2001 , 2BJ A:4001	BINDING SITE FOR RESIDUE 2BJ A 3001
3	AC3	SOFTWARE	HIS A:43 , TRP A:75 , 2BJ A:2001 , 2BJ A:3001	BINDING SITE FOR RESIDUE 2BJ A 4001
4	AC4	SOFTWARE	GLN A:163 , HIS B:43 , LYS B:44 , ALA B:47 , LYS B:48 , VAL B:50 , ARG B:51 , LEU B:88 , ALA B:92 , GLU B:96 , GLN B:168 , HOH B:268 , HOH B:371 , 2BJ B:1001	BINDING SITE FOR RESIDUE 2BJ B 5001
5	AC5	SOFTWARE	MET B:25 , ASP B:26 , GLY B:27 , ASN B:28 , GLY B:29 , HIS B:43 , VAL B:50 , ALA B:69 , LEU B:85 , PHE B:89 , HOH B:284 , HOH B:340 , 2BJ B:5001	BINDING SITE FOR RESIDUE 2BJ B 1001

(no "SS Bond" information available for 3SGV)

(no "Cis Peptide Bond" information available for 3SGV)

(no "SAP(SNP)/Variant" information available for 3SGV)

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 3SGV)

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:222
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:222
                                    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 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFAN 238
               SCOP domains d3sgva_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sgv A  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFAN 238
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236

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

    Alignment length:228
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
           UPPS_ECOLI    13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d3sgvb_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee..-----------hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...........eeeee..........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sgv B  13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAF-----------VSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    22        32        42        52        62       | -        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
                                                                                    70          82

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: Undecaprenyl diphosphate synthase (26)

Protein domain: Undecaprenyl diphosphate synthase (15)

Escherichia coli [TaxId: 562] (13)

1a	d3sgva_	A:
1b	d3sgvb_	B:

(no "CATH Domain" information available for 3SGV)

(no "Pfam Domain" information available for 3SGV)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sgv)

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	3sgv
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	2.5.1.31
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 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)

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Gene Ontology (15, 15)

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