P65932 (PYRH_NEIMB) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Uridylate kinase
Short name=UK
EC=2.7.4.22

Alternative name(s):
Uridine monophosphate kinase
Short name=UMP kinase
Short name=UMPK

Gene names

Name:	pyrH
Ordered Locus Names:	NMB2103

Organism

Neisseria meningitidis serogroup B

Taxonomic identifier

491 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Neisseriales › Neisseriaceae › Neisseria

Protein attributes

Sequence length	239 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible phosphorylation of UMP to UDP. Ref.2
Catalytic activity	ATP + UMP = ADP + UDP. HAMAP MF_01220_B
Enzyme regulation	Allosterically activated by GTP. Inhibited by UTP. Ref.2
Pathway	Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. HAMAP MF_01220_B
Subunit structure	Homohexamer. Ref.2
Subcellular location	Cytoplasm By similarity HAMAP MF_01220_B.
Sequence similarities	Belongs to the UMP kinase family.
Biophysicochemical properties	Kinetic parameters: KM=2.98 mM for ATP (in the absence of GTP) Ref.2 KM=0.83 mM for ATP (in the presence of GTP) KM=8.7 µM for UMP Vmax=35 µmol/min/mg enzyme (in the absence of GTP) Vmax=66 µmol/min/mg enzyme (in the presence of GTP)

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular amino acid biosynthetic process Inferred from electronic annotation. Source: InterPro pyrimidine nucleotide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW UMP kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 239

239

Uridylate kinase HAMAP MF_01220_B

PRO_0000143866

Regions

Nucleotide binding

13 – 16

4

ATP By similarity

Nucleotide binding

136 – 143

8

UMP By similarity

Sites

Binding site

55

1

UMP; via amide nitrogen By similarity

Binding site

56

1

ATP; via amide nitrogen By similarity

Binding site

60

1

ATP By similarity

Binding site

75

1

UMP By similarity

Binding site

163

1

ATP By similarity

Binding site

164

1

ATP By similarity

Binding site

169

1

ATP; via amide nitrogen and carbonyl oxygen By similarity

Binding site

172

1

ATP By similarity

Secondary structure

1

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239

Helix Strand Turn

Details...

Beta strand

8 – 14

7

Helix

16 – 20

5

Beta strand

23 – 26

4

Helix

29 – 44

16

Beta strand

48 – 53

6

Helix

56 – 66

11

Helix

71 – 95

25

Beta strand

100 – 106

7

Beta strand

108 – 111

4

Helix

117 – 125

9

Beta strand

129 – 134

6

Helix

143 – 153

11

Beta strand

157 – 162

6

Beta strand

164 – 167

4

Beta strand

169 – 171

3

Helix

173 – 175

3

Beta strand

183 – 186

4

Helix

187 – 192

6

Helix

200 – 208

9

Beta strand

213 – 216

4

Helix

223 – 229

7

Beta strand

234 – 238

5

Sequences

	Sequence		Length	Mass (Da)
	P65932 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: CB08FD7E1AFBC5FE	FASTA	239	25,700
	10 20 30 40 50 60 MTQQIKYKRV LLKLSGESLM GSDPFGINHD TIVQTVGEIA EVVKMGVQVG IVVGGGNIFR 70 80 90 100 110 120 GVSAQAGSMD RATADYMGMM ATVMNALALK DAFETLGIKA RVQSALSMQQ IAETYARPKA 130 140 150 160 170 180 IQYLEEGKVV IFAAGTGNPF FTTDTAAALR GAEMNCDVML KATNVDGVYT ADPKKDPSAT 190 200 210 220 230 RYETITFDEA LLKNLKVMDA TAFALCRERK LNIVVFGIAK EGSLKRVITG EDEGTLVHC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Neisseria meningitidis serogroup B strain MC58." Tettelin H., Saunders N.J., Heidelberg J.F., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C., Gwinn M.L., DeBoy R.T., Peterson J.D., Hickey E.K., Haft D.H., Salzberg S.L., White O. , Fleischmann R.D., Dougherty B.A., Mason T.M., Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D., Utterback T.R., Khouri H.M., Qin H., Vamathevan J.J., Gill J., Scarlato V., Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M., Moxon E.R., Rappuoli R., Venter J.C. Science 287:1809-1815(2000) [PubMed: 10710307] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MC58 / Serogroup B.
[2]	"Regulatory mechanisms differ in UMP kinases from Gram-negative and Gram-positive bacteria." Evrin C., Straut M., Slavova-Azmanova N., Bucurenci N., Onu A., Assairi L., Ionescu M., Palibroda N., Barzu O., Gilles A.-M. J. Biol. Chem. 282:7242-7253(2007) [PubMed: 17210578] [Abstract] Cited for: FUNCTION, ENZYME REGULATION, KINETIC PARAMETERS, MASS SPECTROMETRY, SUBUNIT.
[3]	"Crystal structure analysis of uridylate kinase from Neisseria meningitidis." New York structural genomics research consortium (NYSGRC) Submitted (FEB-2005) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE002098 Genomic DNA. Translation: AAF42420.1.

PIR

H81006.

RefSeq

NP_275091.1. NC_003112.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YBD	X-ray	2.60	A/B/C	1-239	[»]

ProteinModelPortal

P65932.

SMR

P65932. Positions 4-239.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBNEIT00000009414; EBNEIP00000009034; EBNEIG00000009414.

GeneID

903933.

GenomeReviews

Gene locus NMB2103 in contig AE002098_GR.

KEGG

nme:NMB2103.

PATRIC

20360376. VBINeiMen85645_2685.

TIGR

NMB2103.

Phylogenomic databases

GeneTree

EBGT00050000020791.

HOGENOM

HBG497552.

OMA

RHMEKGR.

ProtClustDB

PRK00358.

Enzyme and pathway databases

BioCyc

NMEN122586:NMB_2103-MONOMER.

Family and domain databases

HAMAP

MF_01220_B. PyrH_B.
[Tree]

InterPro

IPR001048. Asp/Glu/Uridylate_kinase.
IPR011817. Uridylate_kinase.
IPR015963. Uridylate_kinase_bac.
[Graphical view]

Gene3D

G3DSA:3.40.1160.10. Aa_kinase. 1 hit.

KO

K09903.

PANTHER

PTHR26059. PTHR26059. 1 hit.

Pfam

PF00696. AA_kinase. 1 hit.
[Graphical view]

PIRSF

PIRSF005650. Uridylate_kin. 1 hit.

SUPFAM

SSF53633. Aa_kinase. 1 hit.

TIGRFAMs

TIGR02075. PyrH_bact. 1 hit.

ProtoNet

Search...

Entry information

Entry name

PYRH_NEIMB

Accession

Primary (citable) accession number: P65932
Secondary accession number(s): Q9JQT5

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	January 25, 2012
This is version 49 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program