RegulonDB RegulonDB 10.10: Gene Form
   

udp gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rmuC ysgA udp CRP CytR CytR CytR CRP terminator anti-terminator anti-anti-terminator ubiEp2 ubiEp2 ubiEp4 ubiEp4 TSS_4507 TSS_4507 TSS_4506 TSS_4506 TSS_4505 TSS_4505 TSS_4504 TSS_4504 udpP udpP TSS_4503 (cluster) TSS_4503 (cluster) ysgAp ysgAp

Gene      
Name: udp    Texpresso search in the literature
Synonym(s): ECK3825, EG11045, b3831
Genome position(nucleotides): 4016431 --> 4017192 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.07
External database links:  
ASAP:
 ABE-0012528
CGSC:
 41
ECHOBASE:
 EB1038
ECOLIHUB:
 udp
OU-MICROARRAY:
 b3831
STRING:
 511145.b3831
COLOMBOS: udp


Product      
Name: uridine phosphorylase
Synonym(s): Udp
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.159
Isoelectric point: 6.16
Motif(s):
 
Type Positions Sequence
2 -> 253 SKSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL
11 -> 11 L
21 -> 246 LAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVV
5 -> 5 D
15 -> 15 D

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032991 - protein-containing complex
molecular_function GO:0003824 - catalytic activity
GO:0016757 - glycosyltransferase activity
GO:0016740 - transferase activity
GO:0016763 - pentosyltransferase activity
GO:0005524 - ATP binding
GO:0004850 - uridine phosphorylase activity
GO:0030955 - potassium ion binding
GO:0042802 - identical protein binding
biological_process GO:0006218 - uridine catabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0009116 - nucleoside metabolic process
GO:0009166 - nucleotide catabolic process
GO:0044206 - UMP salvage
GO:0046050 - UMP catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Aldea M., et al., 1988
[2] Alkhimova RA., et al., 1981
[3] Alkhimova RA., et al., 1985
[4] Astvatsaturian MZ., et al., 1983
[5] Beacham IR., et al., 1971
[6] Brikun I., et al., 1996
[7] Brikun IA., et al., 1990
[8] Brikun IA., et al., 1989
[9] Brikun IA., et al., 1985
[10] Brikun IA., et al., 1982
[11] Burlakova AA., et al., 1995
[12] Burlakova AA., et al., 1997
[13] Burlakova AA., et al., 1997
[14] Chebotarev DV., et al., 2001
[15] Drabikowska AK., et al., 1987
[16] Drabikowska AK., et al., 1987
[17] Drabikowska AK., et al., 1990
[18] Esipov RS., et al., 2002
[19] Felczak K., et al., 1996
[20] Fonstein M., et al., 1994
[21] Gol'tsmaier TA., et al., 1980
[22] Hammer-Jespersen K., et al., 1975
[23] Hammer-Jespersen K., et al., 1976
[24] Hove-Jensen B. 1988
[25] Komissarov AA., et al., 1994
[26] Krenitsky TA. 1976
[27] Krenitsky TA., et al., 1982
[28] Kulakauskas ST., et al., 1986
[29] Kulakauskas ST., et al., 1985
[30] Kurganov BI., et al., 1997
[31] Kurganov BI., et al., 1997
[32] Liubarev AE., et al., 1998
[33] Lyubarev AE., et al., 1999
[34] Lyubarev AE., et al., 1998
[35] Magni G., et al., 1985
[36] Mihara H., et al., 2008
[37] Mironov AS. 1982
[38] Mironov AS., et al., 1989
[39] Mironov AS., et al., 1975
[40] Mironov AS., et al., 1979
[41] Mushegian AR., et al., 1994
[42] Ovcharova IV., et al., 2004
[43] Paege LM., et al., 1952
[44] Park KS., et al., 1986
[45] Tsuprun VL., et al., 1991
[46] Veiko VP., et al., 1998
[47] Veiko VP., et al., 1995
[48] Veiko VP., et al., 1996
[49] Veiko VP., et al., 1994
[50] Vita A., et al., 1983
[51] Vita A., et al., 1983
[52] Walton L., et al., 1989
[53] Zaporozhets DA., et al., 1996
[54] Zinchenko AI., et al., 1987
[55] Zintchenko AI., et al., 1987
[56] Zolotukhina M., et al., 2003
External database links:  
DIP:
 DIP-11075N
ECOCYC:
 URPHOS-MONOMER
ECOLIWIKI:
 b3831
INTERPRO:
 IPR000845
INTERPRO:
 IPR035994
INTERPRO:
 IPR010058
INTERPRO:
 IPR018016
MINT:
 P12758
MODBASE:
 P12758
PANTHER:
 PTHR43691:SF7
PDB:
 3KVV
PDB:
 1U1D
PDB:
 1U1E
PDB:
 1U1G
PDB:
 1U1F
PDB:
 1K3F
PDB:
 1LX7
PDB:
 1RXC
PDB:
 1RXS
PDB:
 1RXU
PDB:
 1RXY
PDB:
 1T0U
PDB:
 1TGV
PDB:
 1TGY
PDB:
 1U1C
PFAM:
 PF01048
PRIDE:
 P12758
PRODB:
 PRO_000024163
PROSITE:
 PS01232
REFSEQ:
 NP_418275
SMR:
 P12758
UNIPROT:
 P12758


Operon      
Name: udp         
Operon arrangement:
Transcription unit        Promoter
udp


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: CRP, CytR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4503 (cluster) 4016386 forward nd [RS-EPT-CBR] [57]
  promoter TSS_4504 4016393 forward nd [RS-EPT-CBR] [57]
  promoter TSS_4505 4016395 forward nd [RS-EPT-CBR] [57]
  promoter TSS_4506 4016397 forward nd [RS-EPT-CBR] [57]
  promoter TSS_4507 4016404 forward nd [RS-EPT-CBR] [57]
  promoter ubiEp4 4018747 forward nd [ICWHO] [58]
  promoter ubiEp2 4018751 forward nd [ICWHO] [58]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Aldea M., Maples VF., Kushner SR., 1988, Generation of a detailed physical and genetic map of the ilv-metE-udp region of the Escherichia coli chromosome., J Mol Biol 200(3):427-38

 [2] Alkhimova RA., Mironov AS., Sukhodolets VV., 1981, [Regulation of the activity of the Escherichia coli K-12 uridine phosphorylase gene. I. Mapping of the structural gene mutations and a determination of the direction of transcription]., Genetika 17(10):1730-6

 [3] Alkhimova RA., Sukhodolets VV., Mironov AS., 1985, [Enhancement of expression of Escherichia coli uridine phosphorylase gene as a result of duplication]., Genetika 21(5):756-62

 [4] Astvatsaturian MZ., Mironov AS., Sukhodolets VV., 1983, [Mutations of resistance to rifampicin leading to increased activity of the uridine phosphorylase gene in Escherichia coli]., Genetika 19(7):1070-4

 [5] Beacham IR., Pritchard RH., 1971, The role of nucleoside phosphorylases in the degradation of deoxyribonucleosides by thymine-requiring mutants of E. coli., Mol Gen Genet 110(4):289-98

 [6] Brikun I., Suziedelis K., Stemmann O., Zhong R., Alikhanian L., Linkova E., Mironov A., Berg DE., 1996, Analysis of CRP-CytR interactions at the Escherichia coli udp promoter., J Bacteriol 178(6):1614-22

 [7] Brikun IA., Mironov AS., Masiliunaite RV., Sukhodolets VV., 1990, [Cloning of Escherichia coli uridine phosphorylase gene: localization of structural and regulatory regions in the cloned fragment and identification of the protein product]., Mol Gen Mikrobiol Virusol (6):7-11

 [8] Brikun IA., Mironov AS., Sukhodolets VV., Khurges EM., 1989, [Cloning the uridine phosphorylase (udp) gene of Escherichia coli and its expression in recombinant plasmids]., Genetika 25(10):1717-24

 [9] Brikun IA., Sukhodolets VV., 1985, [Characteristics of the phenotypic manifestation of hpt and gpt mutations blocking 6-oxypurine utilization and their effect on the expression of catabolite-sensitive genes in the cells of an Escherichia coli K-12 purine auxotroph]., Genetika 21(6):902-13

 [10] Brikun IA., Sukhodolets VV., 1982, [Effect of mutations in the relC and spoT genes of the "stringent" control regulatory system on the gene expression of Escherichia coli K-12 nucleoside catabolism]., Genetika 18(6):929-38

 [11] Burlakova AA., Komissarov AA., Mikhailov AM., 1995, [Interaction of metal ions with the carboxyl group of Asp-5 in the active site of uridine phosphorylase from Escherichia coli K-12]., Biokhimiia 60(10):1647-53

 [12] Burlakova AA., Kurganov BI., Chebotareva NA., Debabov VG., 1997, Use of hydrated reversed micelles of surfactant in organic solvent for stabilization of individual oligomeric forms of uridine phosphorylase from Escherichia coli K-12., Membr Cell Biol 10(5):543-51

 [13] Burlakova AA., Kurganov BI., Chernyak VYa., Debabov VG., 1997, Denaturation of uridine phosphorylase from Escherichia coli K-12 with guanidine hydrochloride: kinetics of inactivation, dissociation, and reactivation of the enzyme., Biochemistry (Mosc) 62(1):95-103

 [14] Chebotarev DV., Gul'ko LB., Veiko VP., 2001, [Protein engineering of uridine phosphorylase from Escherichia coli K-12. II. Comparative study of hybrid and mutant forms of uridine phosphorylases]., Bioorg Khim 27(3):184-90

 [15] Drabikowska AK., Lissowska L., Draminski M., Zgit-Wroblewska A., Shugar D., 1987, Acyclonucleoside analogues consisting of 5- and 5,6-substituted uracils and different acyclic chains: inhibitory properties vs purified E. coli uridine phosphorylase., Z Naturforsch C 42(3):288-96

 [16] Drabikowska AK., Lissowska L., Veres Z., Shugar D., 1987, Inhibitor properties of some 5-substituted uracil acyclonucleosides, and 2,2'-anhydrouridines versus uridine phosphorylase from E. coli and mammalian sources., Biochem Pharmacol 36(23):4125-8

 [17] Drabikowska AK., Wozniak G., 1990, Modification of uridine phosphorylase from Escherichia coli by diethyl pyrocarbonate. Evidence for a histidine residue in the active site of the enzyme., Biochem J 270(2):319-23

 [18] Esipov RS., Gurevich AI., Chuvikovsky DV., Chupova LA., Muravyova TI., Miroshnikov AI., 2002, Overexpression of Escherichia coli genes encoding nucleoside phosphorylases in the pET/Bl21(DE3) system yields active recombinant enzymes., Protein Expr Purif 24(1):56-60

 [19] Felczak K., Drabikowska AK., Vilpo JA., Kulikowski T., Shugar D., 1996, 6-Substituted and 5,6-disubstituted derivatives of uridine: stereoselective synthesis, interaction with uridine phosphorylase, and in vitro antitumor activity., J Med Chem 39(8):1720-8

 [20] Fonstein M., Nikolskaya T., Zaporojets D., Nikolsky Y., Kulakauskas S., Mironov A., 1994, Tn10-mediated inversions fuse uridine phosphorylase (udp) and rRNA genes of Escherichia coli., J Bacteriol 176(8):2265-71

 [21] Gol'tsmaier TA., Mironov AS., Sukhodolets VV., 1980, [Effect of the ts 15 mutation of transcription termination factor rho on expression of the uridine phosphorylase gene of Escherichia coli]., Genetika 16(4):597-601

 [22] Hammer-Jespersen K., Munch-Ptersen A., 1975, Multiple regulation of nucleoside catabolizing enzymes: regulation of the deo operon by the cytR and deoR gene products., Mol Gen Genet 137(4):327-35

 [23] Hammer-Jespersen K., Nygaard P., 1976, Multiple regulation of nucleoside catabolizing enzymes in Escherichia coli: effects of 3:5' cyclic AMP and CRP protein., Mol Gen Genet 148(1):49-55

 [24] Hove-Jensen B., 1988, Mutation in the phosphoribosylpyrophosphate synthetase gene (prs) that results in simultaneous requirements for purine and pyrimidine nucleosides, nicotinamide nucleotide, histidine, and tryptophan in Escherichia coli., J Bacteriol 170(3):1148-52

 [25] Komissarov AA., Romanova DV., Dmitrieva NA., Linkova EV., Mironov AS., Debabov VG., 1994, Selective modification of putative uridine-binding site of uridine phosphorylase from E. coli with fluorescein 5'-isothiocyanate., Biochim Biophys Acta 1205(1):54-8

 [26] Krenitsky TA., 1976, Uridine phosphorylase from Escherichia coli. Kinetic properties and mechanism., Biochim Biophys Acta 429(2):352-8

 [27] Krenitsky TA., Tuttle JV., 1982, Correlation of substrate-stabilization patterns with proposed mechanisms for three nucleoside phosphorylases., Biochim Biophys Acta 703(2):247-9

 [28] Kulakauskas ST., Mironov AS., Sukhodolets VV., 1986, [Inversion of the metE-oriC-rpsE chromosome segment in Escherichia coli K12]., Genetika 22(11):2649-57

 [29] Kulakauskas ST., Sukhodolets VV., Mironov AS., 1985, [Chromosomal inversion accompanied by an enhancement of uridine phosphorylase gene expression in Escherichia coli K-12]., Genetika 21(3):375-83

 [30] Kurganov BI., Burlakova AA., Chebotareva NA., Debabov VG., 1997, Behavior of uridine phosphorylase from Escherichia coli K-12 in hydrated reversed micelles of surfactant in organic solvent., Biochem Mol Biol Int 41(3):547-54

 [31] Kurganov BI., Burlakova AA., Chernyak VYa., Debabov VG., 1997, Denaturation of uridine phosphorylase from Escherichia coli K-12 by guanidine hydrochloride., Biochem Mol Biol Int 41(6):1191-9

 [32] Liubarev AE., Kurganov BI., Burlakova AA., Orlov VN., Poglazov BF., 1998, [Differential scanning calorimetric study of irreversible heat denaturation of uridine phosphorylase from Escherichia coli K-12]., Dokl Akad Nauk 358(6):830-2

 [33] Lyubarev AE., Kurganov BI., 1999, Modeling of irreversible thermal protein denaturation at varying temperature. II. The complete kinetic model of Lumry and Eyring., Biochemistry (Mosc) 64(7):832-8

 [34] Lyubarev AE., Kurganov BI., Burlakova AA., Orlov VN., 1998, Irreversible thermal denaturation of uridine phosphorylase from Escherichia coli K-12., Biophys Chem 70(3):247-57

 [35] Magni G., Vita A., Amici A., 1985, Pyrimidine nucleoside-catabolizing enzymes in Escherichia coli B., Curr Top Cell Regul 26:433-43

 [36] Mihara H., Hidese R., Yamane M., Kurihara T., Esaki N., 2008, The iscS gene deficiency affects the expression of pyrimidine metabolism genes., Biochem Biophys Res Commun 372(3):407-11

 [37] Mironov AS., 1982, [Regulation of uridine phosphorylase gene activity in Escherichia coli K-12. II. A study of the nature of the constitutive synthesis of uridine phosphorylase in the rho15(ts) genome]., Genetika 18(6):939-46

 [38] Mironov AS., Nechaeva GD., Sukhodolets VV., 1989, [Interaction of negative (CytT) and positive (cAMP-CRP) regulation in the promoter region of the uridine phosphorylase (udp) gene in Escherichia coli K-12]., Genetika 25(3):438-47

 [39] Mironov AS., Smirnov IuV., Sukhodolets VV., 1975, [A further study of the nature of phenotypical reversions in thymidine phosphorylase deletion mutants of Escherichia coli K-12]., Genetika 11(4):97-105

 [40] Mironov AS., Sukhodolets VV., 1979, Promoter-like mutants with increased expression of the Escherichia coli uridine phosphorylase structural gene., J Bacteriol 137(2):802-10

 [41] Mushegian AR., Koonin EV., 1994, Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity., Protein Sci 3(7):1081-8

 [42] Ovcharova IV., Eremina SIu., Mironov AS., 2004, [Structural-functional analysis of the promoter region of Escherichia coli udp gene]., Genetika 40(1):15-25

 [43] Paege LM., Schlenk F., 1952, Bacterial uracil riboside phosphorylase., Arch Biochem Biophys 40(1):42-9

 [44] Park KS., el Kouni MH., Krenitsky TA., Chu SH., Cha S., 1986, Inhibition of uridine phosphorylase from Escherichia coli by benzylacyclouridines., Biochem Pharmacol 35(21):3853-5

 [45] Tsuprun VL., Tagunova IV., Lin'kova EV., Mironov AS., 1991, [Quaternary structure of uridine phosphorylase from E. coli K-12]., Biokhimiia 56(5):930-4

 [46] Veiko VP., Chebotaev DV., Ovcharova IV., Gul'ko LB., 1998, [Protein engineering of uridine phosphorylase from Escherichia coli K-12. I. Cloning and expression of uridine phosphorylase genes from Klebsiella aerogenes and Salmonella typhimurium in E. coli]., Bioorg Khim 24(5):381-7

 [47] Veiko VP., Siprashvili ZZ., Ratmanova KI., Gul'ko LB., 1995, [Study of the role of histidine residues in the function of uridine phosphorylase from Escherichia coli K-12 by protein engineering]., Bioorg Khim 21(11):834-7

 [48] Veiko VP., Siprashvili ZZ., Ratmanova KI., Gul'ko LB., Mironov AA., 1996, [Protein engineering of uridine phosphorylase from Escherichia coli K-12. Study of the role of cysteine residues in enzyme function]., Mol Biol (Mosk) 30(1):170-6

 [49] Veiko VP., Siprashvili ZZ., Ratmanova KI., Gul'ko LB., Mironov AA., Andriukhina RV., Debabov VG., 1994, [Structure-function organization of uridine phosphorylase from Escherichia coli]., Dokl Akad Nauk 339(6):819-21

 [50] Vita A., Amici A., Magni G., 1983, Induction of pyrimidine nucleoside metabolizing enzymes in E. coli B., Ital J Biochem 32(3):145-51

 [51] Vita A., Magni G., 1983, A one-step procedure for the purification of uridine phosphorylase from Escherichia coli., Anal Biochem 133(1):153-6

 [52] Walton L., Richards CA., Elwell LP., 1989, Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene., Nucleic Acids Res 17(16):6741

 [53] Zaporozhets DA., Mironov AS., 1996, [Physical mapping of Escherichia coli genome rearrangements using pulsed-field gel electrophoresis and the PCR method]., Genetika 32(1):23-34

 [54] Zinchenko AI., Barai VN., Eroshevskaia LA., Beigel'man LN., Mikhailov SN., 1987, [2',3'- and 5'-methyl analogs of uridine in the reaction of microbiologic transglycosylation]., Dokl Akad Nauk SSSR 297(3):731-4

 [55] Zintchenko AI., Eroshevskaya LA., Barai VN., Mikhailopulo IA., 1987, Substrate specificity of uridine and purine nucleoside phosphorylases of the whole cells of Escherichia coli., Nucleic Acids Symp Ser (18):137-40

 [56] Zolotukhina M., Ovcharova I., Eremina S., Errais Lopes L., Mironov AS., 2003, Comparison of the structure and regulation of the udp gene of Vibrio cholerae, Yersinia pseudotuberculosis, Salmonella typhimurium, and Escherichia coli., Res Microbiol 154(7):510-20

 [57] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [58] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

RegulonDB