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HAMAP rule MF_01220

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General rule information [?]

Accession MF_01220
Dates 13-AUG-2002 (Created)
17-JAN-2023 (Last updated, Version 28)
Name PyrH
Scope
Bacteria
Archaea
Templates P0A7E9 (PYRH_ECOLI); O31749 (PYRH_BACSU); Q9PPX6 (PYRH_UREPA); Q8U122 (PYRH_PYRFU); Q97ZE2 (PYRH_SACS2); Q97R83 (PYRH_STRPN); P65933 (PYRH_SALTY); P43890 (PYRH_HAEIN); P65932 (PYRH_NEIMB); Q831V1 (PYRH_ENTFA); Q2FZ22 (PYRH_STAA8); P65938 (PYRH_STRP1); O28237 (PYRH_ARCFU); Q9Z5K8 (PYRH_LACLM): [Recover all]
case <OC:Bacteria>
Triggered by
end case

case <OC:Archaea>
Triggered by
end case


Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
PYRH
Protein name
RecName: Full=Uridylate kinase;
Short=UK;
EC 2.7.4.22;
AltName: Full=Uridine monophosphate kinase;
Short=UMP kinase;
Short=UMPK;
Gene name
pyrH

Comments [?]

Function Catalyzes the reversible phosphorylation of UMP to UDP.
Catalytic activity RHEA:24400: ATP + UMP = ADP + UDP
EC 2.7.4.22
case <FT:3>
Activity regulation Allosterically activated by GTP. Inhibited by UTP.
else
Activity regulation Inhibited by UTP.
end case
Pathway Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1.
Subunit Homohexamer.
Subcellular location Cytoplasm.
Similarity Belongs to the UMP kinase family.

Keywords [?]

case <FT:3>
Allosteric enzyme
end case
ATP-binding
Cytoplasm
Kinase
Nucleotide-binding
Pyrimidine biosynthesis
Transferase

Gene Ontology [?]

GO:0009041; Molecular function: uridylate kinase activity.
GO:0006221; Biological process: pyrimidine nucleotide biosynthetic process.
GO:0005737; Cellular component: cytoplasm.

Cross-references [?]

Pfam PF00696; AA_kinase; 1;
TIGRFAMs TIGR02075; PyrH_bact; 1;
TIGR02076; PyrH_arch; 1;

Features [?]

case <OC:Bacteria>
From: PYRH_ECOLI (P0A7E9)
Key     From     To       Description   Tag   Condition   FTGroup
BINDING     15     18       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     K-x-[SG]-G  
BINDING     138     145       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865        
REGION (Optional)     23     28       Involved in allosteric activation by GTP     G-x-x-G-x-G  
BINDING     57     57       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865     G  
BINDING     58     58       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     G  
BINDING     62     62       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     R  
BINDING     77     77       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865     D  
BINDING (Optional)     165     165       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     T  
BINDING (Optional)     166     166       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [NQ]  
BINDING     171     171       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [YF]  
BINDING     174     174       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [DE]  
end case
case <OC:Archaea>
From: PYRH_SACS2 (Q97ZE2)
BINDING (Optional)     7     11       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     K-x-[ST]-G-[KRS]  
BINDING     114     120       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865        
BINDING     44     44       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865     G  
BINDING     66     66       /ligand="UMP" /ligand_id="ChEBI:CHEBI:57865     D  
BINDING     45     45       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     G  
BINDING     49     49       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     R  
BINDING (Optional)     140     140       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [TS]  
BINDING (Optional)     141     141       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     N  
BINDING     146     146       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [YF]  
BINDING     149     149       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [DE]  
end case
case <OC:Archaea> and not <FT:12>
From: PYRH_PYRFU (Q8U122)
BINDING     9     10       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     G-S  
end case

Additional information [?]

case <OC:Bacteria>
Size range 231-266 amino acids
end case
case <OC:Archaea>
Size range 217-241 amino acids
end case
Related rules None
Fusion None
Comments Archaea (SACS2) and UREPA are shown not to be allosterically activated by GTP. This may be due to the absence of a little region containing the motif GXXGXG in the N-terminal part of the enzyme, which could be involved in activation by GTP (see PubMed:18021254). Thus, the activation is automatically annotated via the presence/absence of this region, but the motif GXXGXG is maybe too strict, since NEIMB, that possesses the motif GSDPFG is also shown to be activated by GTP. Two magnesium ions are seen in the catalytic site of PYRFU, but only one in that of SACS2, which binds the phosphate groups of both ATP and UMP. Magnesium 1 annotated in PYRFU could have a catalytic role in the phosphoryl group transfer, a role that could be taken in charge by a positively charged lysine residue in bacteria (Lys-15 in ECOLI) and some other archaea (included SACS2) (see PubMed:17297917). Since the exact catalytic mechanism is not very clear yet and the residues that bind magnesium are not well conserved, this is not annotated and propagated by the rule. Possible wrong start in DEIRA and SYNY3. Longer C-terminus in MALP2; sequence not taken into account in size range.


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