ID LOGH_MYCTU Reviewed; 187 AA.
AC O05306; F2GFY3; I6XAX7; Q7D8M2;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 27-MAR-2024, entry version 130.
DE RecName: Full=Cytokinin riboside 5'-monophosphate phosphoribohydrolase {ECO:0000303|PubMed:25728768};
DE EC=3.2.2.n1 {ECO:0000269|PubMed:25728768};
DE AltName: Full=Protein LONELY GUY homolog {ECO:0000303|PubMed:25728768};
DE Short=LOG homolog {ECO:0000303|PubMed:25728768};
GN Name=log {ECO:0000303|PubMed:25728768};
GN OrderedLocusNames=Rv1205 {ECO:0000312|EMBL:CCP43961.1},
GN RVBD_1205 {ECO:0000312|EMBL:AFN49109.1};
GN ORFNames=P425_01253 {ECO:0000312|EMBL:KBJ36218.1};
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RG The Broad Institute Genome Sequencing Platform;
RA Galagan J., Kreiswirth B., Dobos K., Fortune S., Fitzgerald M., Young S.K.,
RA Zeng Q., Gargeya S., Abouelleil A., Alvarado L., Berlin A.M., Chapman S.B.,
RA Gainer-Dewar J., Goldberg J., Gnerre S., Griggs A., Gujja S., Hansen M.,
RA Howarth C., Imamovic A., Larimer J., McCowan C., Murphy C., Pearson M.,
RA Poon T., Priest M., Roberts A., Saif S., Shea T., Sykes S., Wortman J.,
RA Nusbaum C., Birren B.;
RT "The genome sequence of Mycobacterium tuberculosis H37Rv.";
RL Submitted (NOV-2013) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RG The Broad Institute Genomics Platform;
RG The Broad Institute Genome Sequencing Center for Infectious Disease;
RA Earl A.M., Kreiswirth B., Gomez J., Victor T., Desjardins C., Abeel T.,
RA Young S., Zeng Q., Gargeya S., Abouelleil A., Alvarado L., Chapman S.B.,
RA Gainer-Dewar J., Goldberg J., Griggs A., Gujja S., Hansen M., Howarth C.,
RA Imamovic A., Larimer J., Murphy C., Naylor J., Pearson M., Poon T.W.,
RA Priest M., Roberts A., Saif S., Shea T., Sykes S., Wortman J., Nusbaum C.,
RA Birren B.;
RT "The genome sequence of Mycobacterium tuberculosis H37Rv.";
RL Submitted (APR-2014) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011445;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, PROTEASOME SUBSTRATE, PUPYLATION AT LYS-74, DISRUPTION
RP PHENOTYPE, MUTAGENESIS OF MET-54; LYS-74; GLU-80; ARG-98; 120-ASP-GLU-121
RP AND THR-118, AND SUBUNIT.
RX PubMed=25728768; DOI=10.1016/j.molcel.2015.01.024;
RA Samanovic M.I., Tu S., Novak O., Iyer L.M., McAllister F.E., Aravind L.,
RA Gygi S.P., Hubbard S.R., Strnad M., Darwin K.H.;
RT "Proteasomal control of cytokinin synthesis protects Mycobacterium
RT tuberculosis against nitric oxide.";
RL Mol. Cell 57:984-994(2015).
CC -!- FUNCTION: Catalyzes the hydrolytic removal of ribose 5'-monophosphate
CC from nitrogen N6-modified adenosines, the final step of bioactive
CC cytokinin synthesis. Is involved in the synthesis of isopentenyladenine
CC (iP) and 2-methylthio-iP (2MeS-iP), the most abundant cytokinins
CC detected in M.tuberculosis lysates and supernatants. Is also able to
CC convert trans-zeatin-riboside monophosphate (tZRMP) to trans-zeatin
CC (tZ) in vitro; however, it may not be involved in the biosynthesis of
CC this minor cytokinin in vivo. Accumulation of Rv1205 sensitizes
CC M.tuberculosis to nitric oxide since cytokinin breakdown products
CC synergize with NO to kill M.tuberculosis. Shows a slow AMP hydrolase
CC activity, but is not able to hydrolyze ATP. Displays no lysine
CC decarboxylase (LDC) activity (L-lysine conversion to cadaverine).
CC {ECO:0000269|PubMed:25728768}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-(dimethylallyl)adenosine 5'-phosphate = D-ribose 5-
CC phosphate + N(6)-dimethylallyladenine; Xref=Rhea:RHEA:48560,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17660, ChEBI:CHEBI:57526,
CC ChEBI:CHEBI:78346; EC=3.2.2.n1;
CC Evidence={ECO:0000269|PubMed:25728768};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=9-ribosyl-trans-zeatin 5'-phosphate + H2O = D-ribose 5-
CC phosphate + trans-zeatin; Xref=Rhea:RHEA:48564, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:16522, ChEBI:CHEBI:78346, ChEBI:CHEBI:87947; EC=3.2.2.n1;
CC Evidence={ECO:0000269|PubMed:25728768};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.59 uM for isopentenyladenine riboside monophosphate (iPRMP)
CC {ECO:0000269|PubMed:25728768};
CC KM=73.06 uM for AMP {ECO:0000269|PubMed:25728768};
CC Note=kcat is 434.3 min(-1) for the hydrolysis of iPRMP. kcat is 2.27
CC min(-1) for the hydrolysis of AMP. {ECO:0000269|PubMed:25728768};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:25728768}.
CC -!- PTM: Pupylated at Lys-74 by the prokaryotic ubiquitin-like protein Pup,
CC which leads to its degradation by the proteasome. The proteasomal
CC control of cytokinin synthesis is essential to protect M.tuberculosis
CC against host-produced NO. {ECO:0000269|PubMed:25728768}.
CC -!- DISRUPTION PHENOTYPE: Disruption of this gene suppresses the NO-
CC sensitive phenotype of an mpa mutant, and therefore restores NO
CC resistance to a proteasomal-degradation-deficient M.tuberculosis
CC strain. In addition, the disruption mutation in Rv1205 partially
CC rescues the defective growth of the mpa mutant in the lungs and spleens
CC of mice. Strains lacking Rv1205 show a significant reduction in the
CC amount of several cytokinins: iP levels are almost 30 times lower in
CC mutant supernatants, along with a corresponding increase in the
CC concentration of the cytokinin precursors, and the level of 2MeS-iP is
CC reduced by almost two orders of magnitude in these strains.
CC {ECO:0000269|PubMed:25728768}.
CC -!- SIMILARITY: Belongs to the LOG family. {ECO:0000305}.
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DR EMBL; AL123456; CCP43961.1; -; Genomic_DNA.
DR EMBL; CP003248; AFN49109.1; -; Genomic_DNA.
DR EMBL; JLDD01000013; KBJ36218.1; -; Genomic_DNA.
DR RefSeq; NP_215721.1; NC_000962.3.
DR RefSeq; WP_003898770.1; NZ_NVQJ01000039.1.
DR AlphaFoldDB; O05306; -.
DR SMR; O05306; -.
DR STRING; 83332.Rv1205; -.
DR PaxDb; 83332-Rv1205; -.
DR DNASU; 886075; -.
DR GeneID; 45425175; -.
DR GeneID; 886075; -.
DR KEGG; mtu:Rv1205; -.
DR KEGG; mtv:RVBD_1205; -.
DR PATRIC; fig|83332.111.peg.1347; -.
DR TubercuList; Rv1205; -.
DR eggNOG; COG1611; Bacteria.
DR HOGENOM; CLU_058336_4_0_11; -.
DR InParanoid; O05306; -.
DR OrthoDB; 9801098at2; -.
DR PhylomeDB; O05306; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0016799; F:hydrolase activity, hydrolyzing N-glycosyl compounds; IDA:UniProtKB.
DR GO; GO:0102682; F:N6-(Delta2-isopentenyl)-adenosine 5'-monophosphate phosphoribohydrolase activity; IEA:RHEA.
DR GO; GO:0009691; P:cytokinin biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.40.50.450; -; 1.
DR InterPro; IPR005269; LOG.
DR InterPro; IPR031100; LOG_fam.
DR NCBIfam; TIGR00730; Rossman fold protein, TIGR00730 family; 1.
DR PANTHER; PTHR31223; LOG FAMILY PROTEIN YJL055W; 1.
DR PANTHER; PTHR31223:SF11; LOG FAMILY PROTEIN YJL055W; 1.
DR Pfam; PF03641; Lysine_decarbox; 1.
DR SUPFAM; SSF102405; MCP/YpsA-like; 1.
PE 1: Evidence at protein level;
KW Cytokinin biosynthesis; Hydrolase; Isopeptide bond; Reference proteome;
KW Ubl conjugation.
FT CHAIN 1..187
FT /note="Cytokinin riboside 5'-monophosphate
FT phosphoribohydrolase"
FT /id="PRO_0000433000"
FT BINDING 80
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B2HS63"
FT BINDING 98..99
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B2HS63"
FT BINDING 115..121
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B2HS63"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B2HS63"
FT CROSSLNK 74
FT /note="Isoglutamyl lysine isopeptide (Lys-Gln) (interchain
FT with Q-Cter in protein Pup)"
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 54
FT /note="M->A: Large decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 74
FT /note="K->A: Abrogates pupylation. This mutant accumulates
FT in M.tuberculosis with a functional proteasome system and
FT sensitizes M.tuberculosis to NO. Decrease in catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 80
FT /note="E->A: Large decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 98
FT /note="R->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 118
FT /note="T->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:25728768"
FT MUTAGEN 120..121
FT /note="DE->AA: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:25728768"
SQ SEQUENCE 187 AA; 20014 MW; 892D09FFD6935D23 CRC64;
MSAKIDITGD WTVAVYCAAS PTHAELLELA AEVGAAIAGR GWTLVWGGGH VSAMGAVASA
ARACGGWTVG VIPKMLVYRE LADHDADELI VTDTMWERKQ IMEDRSDAFI VLPGGVGTLD
ELFDAWTDGY LGTHDKPIVM VDPWGHFDGL RAWLNGLLDT GYVSPTAMER LVVVDNVKDA
LRACAPS
//
