O82827 (UPPS_MICLU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
EC=2.5.1.31

Alternative name(s):
Ditrans,polycis-undecaprenylcistransferase
Undecaprenyl diphosphate synthase
Short name=UDS
Undecaprenyl pyrophosphate synthase
Short name=UPP synthase

Gene names

Name:

uppS

Organism

Micrococcus luteus (Micrococcus lysodeikticus)

Taxonomic identifier

1270 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Micrococcineae › Micrococcaceae › Micrococcus

Protein attributes

Sequence length	249 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate. UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide. Ref.1 Ref.2
Catalytic activity	(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + di-trans,octa-cis-undecaprenyl diphosphate. Ref.1
Cofactor	Binds 2 magnesium ions per subunit By similarity.
Subunit structure	Homodimer. Ref.7
Domain	This enzyme shows a novel protein fold completely different from the "isoprenoid synthase fold" that is thought to be a common structure for the enzymes relating to isoprenoid biosynthesis. HAMAP-Rule MF_01139
Sequence similarities	Belongs to the UPP synthase family.

Ontologies

Keywords
Ligand	Magnesium Metal-binding
Molecular function	Transferase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Molecular_function	di-trans,poly-cis-decaprenylcistransferase activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 249

249

Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) HAMAP-Rule MF_01139

PRO_0000123637

Regions

Region

30 – 33

4

Substrate binding HAMAP-Rule MF_01139

Region

74 – 76

3

Substrate binding By similarity

Region

203 – 205

3

Substrate binding By similarity

Sites

Active site

29

1

Active site

77

1

Proton acceptor By similarity

Metal binding

29

1

Magnesium By similarity

Metal binding

216

1

Magnesium By similarity

Binding site

34

1

Substrate By similarity

Binding site

42

1

Substrate

Binding site

46

1

Substrate By similarity

Binding site

78

1

Substrate By similarity

Binding site

80

1

Substrate By similarity

Binding site

197

1

Substrate By similarity

Experimental info

Mutagenesis

29

1

D → A: Great decrease in activity. Ref.5

Mutagenesis

32

1

G → R: Great decrease in activity. Decrease in activity; when associated with G-42. Ref.5

Mutagenesis

33

1

R → A: Decrease in affinity for decaprenyl diphosphate substrate analog. Ref.5

Mutagenesis

42

1

R → G: Great decrease in activity. Decrease in activity; when associated with R-32. Ref.5

Mutagenesis

73

1

F → A: Decrease in activity; reduced affinity for substrate. Ref.4

Mutagenesis

74

1

S → A: Decrease in activity; reduced affinity for substrate. Ref.4

Mutagenesis

76

1

E → Q: Slight decrease in activity. Ref.5

Mutagenesis

77

1

N → A, D or Q: Great decrease in activity. Ref.3

Mutagenesis

78

1

W → I, R or D: Decrease in activity. Ref.3

Mutagenesis

80

1

R → A: Great decrease in activity. Ref.5

Mutagenesis

84

1

E → Q: Slight decrease in activity. Ref.5

Mutagenesis

193

1

E → Q: Decrease in activity. Ref.4

Mutagenesis

197

1

R → S: Great decrease in activity; reduced affinity for substrate. Ref.4

Mutagenesis

201

1

E → Q: Slight decrease in activity. Ref.4

Mutagenesis

203

1

R → S: Great decrease in activity; reduced affinity for substrate. Ref.4

Mutagenesis

216

1

E → Q: Great decrease in activity; reduced affinity for substrate. Ref.4

Mutagenesis

221

1

D → A: Decrease in activity. Ref.4

Mutagenesis

226

1

D → A: Slight decrease in activity. Ref.4

Secondary structure

1

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249

Helix Strand Turn

Details...

Beta strand

22 – 28

7

Helix

31 – 37

7

Helix

42 – 63

22

Beta strand

67 – 72

6

Helix

87 – 89

3

Helix

91 – 105

15

Beta strand

109 – 114

6

Helix

116 – 118

3

Helix

121 – 132

12

Turn

133 – 136

4

Beta strand

141 – 145

5

Helix

150 – 166

17

Helix

172 – 174

3

Helix

177 – 180

4

Helix

181 – 183

3

Turn

185 – 188

4

Beta strand

193 – 197

5

Turn

209 – 214

6

Beta strand

216 – 219

4

Helix

224 – 226

3

Helix

229 – 239

11

Sequences

	Sequence		Length	Mass (Da)
	O82827 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 044F7DD77745AEEE	FASTA	249	28,876
	10 20 30 40 50 60 MFPIKKRKAI KNNNINAAQI PKHIAIIMDG NGRWAKQKKM PRIKGHYEGM QTVKKITRYA 70 80 90 100 110 120 SDLGVKYLTL YAFSTENWSR PKDEVNYLMK LPGDFLNTFL PELIEKNVKV ETIGFIDDLP 130 140 150 160 170 180 DHTKKAVLEA KEKTKHNTGL TLVFALNYGG RKEIISAVQL IAERYKSGEI SLDEISETHF 190 200 210 220 230 240 NEYLFTANMP DPELLIRTSG EERLSNFLIW QCSYSEFVFI DEFWPDFNEE SLAQCISIYQ NRHRRFGGL

References

[1]	"Molecular cloning, expression, and purification of undecaprenyl diphosphate synthase. No sequence similarity between E- and Z-prenyl diphosphate synthases." Shimizu N., Koyama T., Ogura K. J. Biol. Chem. 273:19476-19481(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-14, FUNCTION AS AN UNDECAPRENYL DIPHOSPHATE SYNTHASE, CATALYTIC ACTIVITY. Strain: B-P 26.
[2]	"Undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26: essential factors for the enzymatic activity." Koyama T., Yoshida I., Ogura K. J. Biochem. 103:867-871(1988) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS AN UNDECAPRENYL DIPHOSPHATE SYNTHASE. Strain: B-P 26.
[3]	"Significance of Asn-77 and Trp-78 in the catalytic function of undecaprenyl diphosphate synthase of Micrococcus luteus B-P 26." Fujikura K., Zhang Y.W., Yoshizaki H., Nishino T., Koyama T. J. Biochem. 128:917-922(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASN-77 AND TRP-78. Strain: B-P 26.
[4]	"Identification of Significant residues for homoallylic substrate binding of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase." Kharel Y., Zhang Y.W., Fujihashi M., Miki K., Koyama T. J. Biol. Chem. 276:28459-28464(2001) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF PHE-73; SER-74; GLU-193; ARG-197; GLU-201; ARG-203; GLU-216; ASP-221 AND ASP-226. Strain: B-P 26.
[5]	"Mutational analysis of allylic substrate binding site of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase." Fujikura K., Zhang Y.-W., Fujihashi M., Miki K., Koyama T. Biochemistry 42:4035-4041(2003) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-29; GLY-32; ARG-33; ARG-42; GLU-76; ARG-80 AND GLU-84. Strain: B-P 26.
[6]	"Crystallization and preliminary X-ray diffraction studies of undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26." Fujihashi M., Shimizu N., Zhang Y.W., Koyama T., Miki K. Acta Crystallogr. D 55:1606-1607(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION. Strain: B-P 26.
[7]	"Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase." Fujihashi M., Zhang Y.-W., Higuchi Y., Li X.-Y., Koyama T., Miki K. Proc. Natl. Acad. Sci. U.S.A. 98:4337-4342(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT. Strain: B-P 26.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB004319 Genomic DNA. Translation: BAA31993.1.

PIR

T48857.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F75	X-ray	2.20	A/B	1-249	[»]

ProteinModelPortal

O82827.

SMR

O82827. Positions 14-242.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.1180.10. 1 hit.

HAMAP

MF_01139. ISPT.

InterPro

IPR001441. UPP_synth-like.
IPR018520. UPP_synth-like_CS.
[Graphical view]

PANTHER

PTHR10291. PTHR10291. 1 hit.

Pfam

PF01255. Prenyltransf. 1 hit.
[Graphical view]

SUPFAM

SSF64005. UPP_synth. 1 hit.

TIGRFAMs

TIGR00055. uppS. 1 hit.

PROSITE

PS01066. UPP_SYNTHASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O82827.

Entry information

Entry name

UPPS_MICLU

Accession

Primary (citable) accession number: O82827

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	November 1, 1998
Last modified:	April 3, 2013
This is version 76 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program