Escherichia coli K-12 substr. MG1655 Enzyme: UMP kinase

Gene: pyrH Accession Numbers: EG11539 (EcoCyc), b0171, ECK0170

Synonyms: umk, smbA

Regulation Summary Diagram: ?

Regulation summary diagram for pyrH

Subunit composition of UMP kinase = [PyrH]6
         UMP kinase = PyrH

UMP kinase (PyrH) is an essential enzyme involved in the de novo biosynthesis of pyrimidine nucleotides. The enzyme is subject to complex regulatory control by GTP and UTP [Serina95]. Feedback inhibition of UMP kinase by UTP is important for an optimal response to nutritional conditions such as growth on orotate [Reaves13].

Temperature-sensitive and site-directed mutants in pyrH have been studied to reveal residues essential for thermodynamic stability, catalysis and allosteric regulation [Serina96, Bucurenci98, Sakamoto04, Meyer08, MarcoMarin09].

Crystal structures of PyrH bound to its substrate, product, competitive inhibitor UTP [Briozzo05] and allosteric regulator GTP [Meyer08] have been solved. The GTP and UTP binding sites do not overlap [Meyer08, MarcoMarin09]. A comparative study of E. coli UMP kinase with UMP kinases from several other Gram-negative and Gram-positive bacteria showed that regulation by GTP and UTP differed, suggesting different recognition sites on the different enzymes [Evrin07].

PyrH appears to play a direct role in the transcriptional regulation of the carAB operon [Kholti98].

SmbA: "suppressor of mukB" [Yamanaka92]

Citations: [Pierard76, Yamanaka94, Labesse02, CornishBowden13]

Locations [Comment 1]: cytosol

Map Position: [191,855 -> 192,580] (4.14 centisomes, 15°)
Length: 726 bp / 241 aa

Molecular Weight of Polypeptide: 25.97 kD (from nucleotide sequence), 28.0 kD (experimental) [Yamanaka92 ]

Molecular Weight of Multimer: 156 kD (experimental) [Serina95]

Unification Links: ASAP:ABE-0000582 , CGSC:324 , DIP:DIP-31830N , EchoBASE:EB1501 , EcoGene:EG11539 , EcoliWiki:b0171 , Mint:MINT-1222953 , ModBase:P0A7E9 , OU-Microarray:b0171 , PortEco:pyrH , PR:PRO_000023663 , Pride:P0A7E9 , Protein Model Portal:P0A7E9 , RefSeq:NP_414713 , RegulonDB:EG11539 , SMR:P0A7E9 , String:511145.b0171 , UniProt:P0A7E9

Relationship Links: InterPro:IN-FAMILY:IPR001048 , InterPro:IN-FAMILY:IPR011817 , InterPro:IN-FAMILY:IPR015963 , Panther:IN-FAMILY:PTHR26059 , PDB:Structure:2BND , PDB:Structure:2BNE , PDB:Structure:2BNF , PDB:Structure:2V4Y , Pfam:IN-FAMILY:PF00696

In Paralogous Gene Group: 1 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006221 - pyrimidine nucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Serina95]
GO:0046939 - nucleotide phosphorylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Serina95]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
GO:0044210 - 'de novo' CTP biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0033862 - UMP kinase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Serina95]
GO:0042802 - identical protein binding Inferred from experiment [Serina95]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0009041 - uridylate kinase activity Inferred by computational analysis [GOA06, GOA01a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Watt07]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for pyrH knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Curated 13-Jan-2012 by Fulcher C , SRI International
Last-Curated ? 22-Aug-2013 by Keseler I , SRI International

Enzymatic reaction of: UMP kinase

Synonyms: UK, uridine monophosphate kinase, uridylate kinase, uridine 5'-monophosphate (UMP) kinase

EC Number:


The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis , superpathway of pyrimidine ribonucleotides de novo biosynthesis , superpathway of pyrimidine ribonucleosides salvage , superpathway of pyrimidine nucleobases salvage , UTP and CTP de novo biosynthesis

Enzymatic activity in the reverse direction is low in vitro (3 U/mg vs. 155 U/mg in the forward direction) [Serina95].

Activators (Allosteric): GTP [Serina95, Meyer08]

Inhibitors (Competitive): UTP (Kic = 154µM) [Briozzo05, Serina95]

Primary Physiological Regulators of Enzyme Activity: GTP , UTP

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of UMP kinase with features indicated

Feature Class Location Attached Group Citations Comment
Cleavage-of-Initial-Methionine 1  
[Serina95, UniProt11]
UniProt: Removed.
Chain 2 -> 241  
UniProt: Uridylate kinase;
Nucleotide-Phosphate-Binding-Region 15 -> 18  
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Protein-Segment 23 -> 28  
UniProt: Involved in allosteric activation by GTP; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 57  
[Briozzo05, UniProt15]
UniProt: UMP; via amide nitrogen.
Amino-Acid-Sites-That-Bind 58  
UniProt: ATP; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Extrinsic-Sequence-Variant 62  
UniProt: In Smba9..
Mutagenesis-Variant 62  
[Bucurenci98, UniProt11]
UniProt: Loss of activation by GTP and decreased affinity for UTP.
Amino-Acid-Sites-That-Bind 62  
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 64 -> 69  
[Smallshaw92, UniProt15]
UniProt: (in Ref. 1; CAA55388).
Amino-Acid-Sites-That-Bind 77  
[Briozzo05, UniProt15]
UniProt: UMP.
Mutagenesis-Variant 77  
[Bucurenci98, UniProt11]
UniProt: Loss of activation by GTP and decreased affinity for UTP.
Nucleotide-Phosphate-Binding-Region 138 -> 145 UMP
[Briozzo05, UniProt15]
UniProt: UMP.
Mutagenesis-Variant 138  
[Briozzo05, UniProt11]
UniProt: Loss of activation by GTP. Moderate loss of sensitivity to UTP inhibition. 4- fold and 2-fold decrease in affinity for UMP and ATP, respectively.
Mutagenesis-Variant 140  
[Briozzo05, UniProt11]
UniProt: Loss of activation by GTP. Moderate loss of sensitivity to UTP inhibition.
Mutagenesis-Variant 146  
[Bucurenci98, UniProt11]
UniProt: Drastically reduced activity.
Mutagenesis-Variant 159  
[Bucurenci98, UniProt11]
UniProt: Increased solubility at neutral pH. Nearly no change in kinetic properties and stability.
Amino-Acid-Sites-That-Bind 165  
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 171  
UniProt: ATP; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 174  
[Bucurenci98, UniProt11]
UniProt: Reduced UMP-binding affinity.
Amino-Acid-Sites-That-Bind 174  
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Extrinsic-Sequence-Variant 201  
UniProt: In Smba2..
Mutagenesis-Variant 201  
[Bucurenci98, Serina95, UniProt11]
UniProt: Loss of activation by GTP.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0171 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11539; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Briozzo05: Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM (2005). "Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation." J Biol Chem 280(27);25533-40. PMID: 15857829

Bucurenci98: Bucurenci N, Serina L, Zaharia C, Landais S, Danchin A, Barzu O (1998). "Mutational analysis of UMP kinase from Escherichia coli." J Bacteriol 180(3);473-7. PMID: 9457846

CornishBowden13: Cornish-Bowden A (2013). "Biochemistry: Curbing the excesses of low demand." Nature 500(7461);157-8. PMID: 23903659

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Evrin07: Evrin C, Straut M, Slavova-Azmanova N, Bucurenci N, Onu A, Assairi L, Ionescu M, Palibroda N, Barzu O, Gilles AM (2007). "Regulatory mechanisms differ in UMP kinases from gram-negative and gram-positive bacteria." J Biol Chem 282(10);7242-53. PMID: 17210578

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kholti98: Kholti A, Charlier D, Gigot D, Huysveld N, Roovers M, Glansdorff N (1998). "pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli." J Mol Biol 280(4);571-82. PMID: 9677289

Labesse02: Labesse G, Bucurenci N, Douguet D, Sakamoto H, Landais S, Gagyi C, Gilles AM, Barzu O (2002). "Comparative modelling and immunochemical reactivity of Escherichia coli UMP kinase." Biochem Biophys Res Commun 294(1);173-9. PMID: 12054759

Landais99: Landais S, Gounon P, Laurent-Winter C, Mazie JC, Danchin A, Barzu O, Sakamoto H (1999). "Immunochemical analysis of UMP kinase from Escherichia coli." J Bacteriol 1999;181(3);833-40. PMID: 9922246

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

MarcoMarin09: Marco-Marin C, Rubio V (2009). "The site for the allosteric activator GTP of Escherichia coli UMP kinase." FEBS Lett 583(1);185-9. PMID: 19071117

Meyer08: Meyer P, Evrin C, Briozzo P, Joly N, Barzu O, Gilles AM (2008). "Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP." J Biol Chem 283(51);36011-8. PMID: 18945668

Pierard76: Pierard A, Glansdorff N, Gigot D, Crabeel M, Halleux P, Thiry L (1976). "Repression of Escherichia coli carbamoylphosphate synthase: relationships with enzyme synthesis in the arginine and pyrimidine pathways." J Bacteriol 127(1);291-301. PMID: 179975

Reaves13: Reaves ML, Young BD, Hosios AM, Xu YF, Rabinowitz JD (2013). "Pyrimidine homeostasis is accomplished by directed overflow metabolism." Nature 500(7461);237-41. PMID: 23903661

Sakamoto04: Sakamoto H, Landais S, Evrin C, Laurent-Winter C, Barzu O, Kelln RA (2004). "Structure-function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria." Microbiology 150(Pt 7);2153-9. PMID: 15256558

Serina95: Serina L, Blondin C, Krin E, Sismeiro O, Danchin A, Sakamoto H, Gilles AM, Barzu O (1995). "Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP." Biochemistry 1995;34(15);5066-74. PMID: 7711027

Serina96: Serina L, Bucurenci N, Gilles AM, Surewicz WK, Fabian H, Mantsch HH, Takahashi M, Petrescu I, Batelier G, Barzu O (1996). "Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP." Biochemistry 35(22);7003-11. PMID: 8679525

Smallshaw92: Smallshaw J.E., Kelln R.A. (1992). "Cloning, nucleotide sequence and expression of the Escherichia coli K-12 pyrH gene encoding UMP kinase." Life Sci. Adv. (Genet.), Volume 11, page(s) 59-65.

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Watt07: Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD (2007). "Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes." Nucleic Acids Res 35(6);e37. PMID: 17272300

Yamanaka92: Yamanaka K, Ogura T, Niki H, Hiraga S (1992). "Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli." J Bacteriol 174(23);7517-26. PMID: 1447125

Yamanaka94: Yamanaka K, Ogura T, Koonin EV, Niki H, Hiraga S (1994). "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli." Mol Gen Genet 243(1);9-16. PMID: 8190075

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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