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Annotation rule MF_01220
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General rule information [?]

Accession MF_01220
Dates 13-AUG-2002 (Created)
19-NOV-2019 (Last updated, Version 25)
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>
end case

case <OC:Archaea>
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>
end case

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
NP_BIND     15     18       ATP     K-x-[SG]-G  
NP_BIND     138     145       UMP        
REGION (Optional)     23     28       Involved in allosteric activation by GTP     G-x-x-G-x-G  
BINDING     57     57       UMP; via amide nitrogen     G  
BINDING     58     58       ATP; via amide nitrogen     G  
BINDING     62     62       ATP     R  
BINDING     77     77       UMP     D  
BINDING (Optional)     165     165       ATP     T  
BINDING (Optional)     166     166       ATP     [NQ]  
BINDING     171     171       ATP; via amide nitrogen and carbonyl oxygen     [YF]  
BINDING     174     174       ATP     [DE]  
end case
case <OC:Archaea>
From: PYRH_SACS2 (Q97ZE2)
NP_BIND (Optional)     7     11       ATP     K-x-[ST]-G-[KRS]  
NP_BIND     114     120       UMP        
BINDING     44     44       UMP; via amide nitrogen     G  
BINDING     66     66       UMP     D  
BINDING     45     45       ATP; via amide nitrogen     G  
BINDING     49     49       ATP     R  
BINDING (Optional)     140     140       ATP     [TS]  
BINDING (Optional)     141     141       ATP     N  
BINDING     146     146       ATP; via amide nitrogen and carbonyl oxygen     [YF]  
BINDING     149     149       ATP     [DE]  
end case
case <OC:Archaea> and not <FT:12>
From: PYRH_PYRFU (Q8U122)
NP_BIND     9     10       ATP     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 MYCPE; sequence not taken into account in size range.