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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	udp
Gene Synonym(s)	ECK3825, b3831, JW3808^[1], JW3808
Product Desc.	Udp^[2]^[3]; Component of uridine phosphorylase^[2]^[3] Uridine phosphorylase^[4]
Product Synonyms(s)	uridine phosphorylase^[1], B3831^[2]^[1], Udp^[2]^[1] , ECK3825, JW3808, b3831
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): udp^[2], OP00178
Regulation/Activity
Quick Links
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Notes

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Binds TrxA (Kumar, 2004).^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	udp
Mnemonic	Uridine phosphorylase
Synonyms	ECK3825, b3831, JW3808^[1], JW3808
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	86.52 minutes	MG1655: 4014454..4015215 <gbrowseImage> name=NC_000913:4014454..4015215 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3989350..3990114 <gbrowseImage> name=NC_012967:3989350..3990114 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3904123..3904884 <gbrowseImage> name=NC_012759:3904123..3904884 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3620250..3619489 <gbrowseImage> name=NC_007779:3619489..3620250 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4113374..4114135 <gbrowseImage> name=NC_010473:4113374..4114135 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	4014457	Edman degradation	PMID:8506346 PMID:18482579
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Δudp (Keio:JW3808)	deletion	deletion		PMID:16738554	Shigen
udpD5A,E,N		D5A,E,N	No change in activity			seeded from UniProt:P12758
udp-1					CGSC:5956
udp-10					CGSC:8637
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3808	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCCAAGTCTGATGTTTTTCA Primer 2:CCaAGCAGACGACGCGCCGCTTC
16G1	Kohara Phage	Genobase	PMID:3038334
1C10	Kohara Phage	Genobase	PMID:3038334
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 82% ^[6] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 64% ^[6] Synonyms:fadAB101::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11045	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11045	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001034	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948987	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1038	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012528	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Udp
Synonyms	uridine phosphorylase^[1], B3831^[2]^[1], Udp^[2]^[1] , ECK3825, JW3808, b3831
Product description	Udp^[2]^[3]; Component of uridine phosphorylase^[2]^[3] Uridine phosphorylase^[4]
EC number (for enzymes)	2.4.2.3^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000845	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004850	uridine phosphorylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010058	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004850	uridine phosphorylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0009116	nucleoside metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000845	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009166	nucleotide catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010058	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016757	transferase activity, transferring glycosyl groups	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0328	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016763	transferase activity, transferring pentosyl groups	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018016	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of uridine phosphorylase	could be indirect
Protein	fdoG		PMID:16606699	Experiment(s):EBI-1146753
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF TTWRAELDGK PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP HINVGDVLVT TASVRLDGAS LHFAPLEFPA VADFECTTAL VEAAKSIGAT THVGVTASSD TFYPGQERYD TYSGRVVRHF KGSMEEWQAM GVMNYEMESA TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH AVKIVVEAAR RLL
Length	253
Mol. Wt	27.158 kDa
pI	6.2 (calculated)
Extinction coefficient	16,960 - 17,335 (calc based on 4 Y, 2 W, and 3 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P12758
Domain	20..253	PF01048 Phosphorylase superfamily		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=udp taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131680	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948987	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012528	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P12758	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11045	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11045	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948987	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001034	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1038	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	6.26E+03	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	2761	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	2011	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	2073	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
udp
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:4014434..4014474 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3831 (EcoliWiki Page)	NCBI GEO profiles for udp
microarray	GenExpDB:b3831 (EcoliWiki Page)	Summary of data for udp from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (4013628..4014073) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:E3^[7]
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Notes

Accessions Related to udp Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11045	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1038	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3831
EcoGene	EcoGene:EG11045	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001034	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012528	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Bos taurus	ENSBTAP00000025944 (score: 1.000; bootstrap: 100%) ENSBTAP00000017006 (score: 0.564)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00023526 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00022817 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000021049 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0230169 (score: 1.000; bootstrap: 91%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039464 (score: 1.000; bootstrap: 100%) FBgn0034800 (score: 0.437) FBgn0031489 (score: 0.305)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19516-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000021316 (score: 1.000; bootstrap: 100%) ENSGALP00000020473 (score: 0.580)	From Inparanoid:20070104
Homo sapiens	ENSP00000330032 (score: 1.000; bootstrap: 100%) ENSP00000005756 (score: 0.580)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000009232 (score: 1.000; bootstrap: 100%) ENSMMUP00000015270 (score: 0.577)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005480 (score: 1.000; bootstrap: 100%) ENSMODP00000011764 (score: 0.545) ENSMODP00000025930 (score: 0.401)	From Inparanoid:20070104
Mus musculus	MGI:1923904 (score: 1.000; bootstrap: 100%) MGI:1097668 (score: 0.563)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000032766 (score: 1.000; bootstrap: 100%) ENSPTRP00000021460 (score: 0.566)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000006765 (score: 1.000; bootstrap: 100%) ENSRNOP00000007121 (score: 0.580)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000142576 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000145183 (score: 0.625)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00034076001 (score: 1.000; bootstrap: 100%) GSTENP00030565001 (score: 0.626) GSTENP00000958001 (score: 0.307)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000034209 (score: 1.000; bootstrap: 100%) ENSXETP00000022798 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	G7V-670	From SHIGELLACYC
E. coli O157	G7E-1	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Panther (EcoliWiki Page)	PTHR21234:SF7
Superfamily (EcoliWiki Page)	SUPERFAMILY:53167
Pfam (EcoliWiki Page)	PF01048 Phosphorylase superfamily
EcoCyc	EcoCyc:EG11045	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11045	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001034	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1038	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012528	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

udp:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to udp Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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