PYRG_MYCTU
ID PYRG_MYCTU Reviewed; 586 AA.
AC P9WHK7; L0TA54; P0A5U2; P96351;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 44.
DE RecName: Full=CTP synthase {ECO:0000255|HAMAP-Rule:MF_01227};
DE EC=6.3.4.2 {ECO:0000255|HAMAP-Rule:MF_01227};
DE AltName: Full=Cytidine 5'-triphosphate synthase {ECO:0000255|HAMAP-Rule:MF_01227};
DE AltName: Full=Cytidine triphosphate synthetase {ECO:0000255|HAMAP-Rule:MF_01227};
DE Short=CTP synthetase {ECO:0000255|HAMAP-Rule:MF_01227, ECO:0000303|PubMed:26097035};
DE Short=CTPS {ECO:0000255|HAMAP-Rule:MF_01227};
DE AltName: Full=UTP--ammonia ligase {ECO:0000255|HAMAP-Rule:MF_01227};
GN Name=pyrG; OrderedLocusNames=Rv1699; ORFNames=MTCI125.21;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; 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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
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 [3]
RP X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP UTP; AMP-PCP AND OXONORLEUCINE, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, SUBUNIT, MUTAGENESIS OF
RP VAL-186, AND ACTIVE SITE.
RC STRAIN=H37Rv;
RX PubMed=26097035; DOI=10.1016/j.chembiol.2015.05.016;
RA Mori G., Chiarelli L.R., Esposito M., Makarov V., Bellinzoni M.,
RA Hartkoorn R.C., Degiacomi G., Boldrin F., Ekins S.,
RA de Jesus Lopes Ribeiro A.L., Marino L.B., Centarova I., Svetlikova Z.,
RA Blasko J., Kazakova E., Lepioshkin A., Barilone N., Zanoni G., Porta A.,
RA Fondi M., Fani R., Baulard A.R., Mikusova K., Alzari P.M., Manganelli R.,
RA de Carvalho L.P., Riccardi G., Cole S.T., Pasca M.R.;
RT "Thiophenecarboxamide derivatives activated by EthA kill Mycobacterium
RT tuberculosis by inhibiting the CTP synthetase PyrG.";
RL Chem. Biol. 22:917-927(2015).
CC -!- FUNCTION: Catalyzes the ATP-dependent amination of UTP to CTP with
CC either L-glutamine or ammonia as the source of nitrogen. Is essential
CC for M.tuberculosis growth in vitro and ex vivo (PubMed:26097035).
CC Regulates intracellular CTP levels through interactions with the four
CC ribonucleotide triphosphates (By similarity). {ECO:0000255|HAMAP-
CC Rule:MF_01227, ECO:0000269|PubMed:26097035}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-
CC glutamate + phosphate; Xref=Rhea:RHEA:26426, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:37563, ChEBI:CHEBI:43474, ChEBI:CHEBI:46398,
CC ChEBI:CHEBI:58359, ChEBI:CHEBI:456216; EC=6.3.4.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01227,
CC ECO:0000269|PubMed:26097035};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamine = L-glutamate + NH4(+);
CC Xref=Rhea:RHEA:15889, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:58359; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01227};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate;
CC Xref=Rhea:RHEA:16597, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:37563, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:46398, ChEBI:CHEBI:456216; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01227};
CC -!- ACTIVITY REGULATION: Allosterically activated by GTP, when glutamine is
CC the substrate; GTP has no effect on the reaction when ammonia is the
CC substrate. The allosteric effector GTP functions by stabilizing the
CC protein conformation that binds the tetrahedral intermediate(s) formed
CC during glutamine hydrolysis. Inhibited by the product CTP, via
CC allosteric rather than competitive inhibition (By similarity). Is
CC inhibited by the EthA-activated metabolites of compounds 7947882 (5-
CC methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-
CC N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide), that have been
CC shown to have anti-tubercular activity against M.tuberculosis in its
CC replicating, non-replicating, and intracellular states; active
CC metabolites of 7947882 correspond to the S-dioxide and S-monoxide
CC derivatives (PubMed:26097035). One active metabolite was shown to
CC behave as a competitive inhibitor toward the ATP-binding site of PyrG
CC (PubMed:26097035). Direct inhibition of PyrG decreases CTP levels,
CC leading to disruption of the nucleotide metabolic network,
CC characterized by increased levels of several intermediates in the
CC biosynthesis of pyrimidines and purines (PubMed:26097035).
CC {ECO:0000255|HAMAP-Rule:MF_01227, ECO:0000269|PubMed:26097035}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.18 mM for ATP {ECO:0000269|PubMed:26097035};
CC KM=0.14 mM for UTP {ECO:0000269|PubMed:26097035};
CC Note=kcat is 22.9 sec(-1). {ECO:0000269|PubMed:26097035};
CC -!- PATHWAY: Pyrimidine metabolism; CTP biosynthesis via de novo pathway;
CC CTP from UDP: step 2/2. {ECO:0000255|HAMAP-Rule:MF_01227}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01227,
CC ECO:0000269|PubMed:26097035}.
CC -!- MISCELLANEOUS: CTPSs have evolved a hybrid strategy for distinguishing
CC between UTP and CTP. The overlapping regions of the product feedback
CC inhibitory and substrate sites recognize a common feature in both
CC compounds, the triphosphate moiety. To differentiate isosteric
CC substrate and product pyrimidine rings, an additional pocket far from
CC the expected kinase/ligase catalytic site, specifically recognizes the
CC cytosine and ribose portions of the product inhibitor.
CC {ECO:0000255|HAMAP-Rule:MF_01227}.
CC -!- SIMILARITY: Belongs to the CTP synthase family. {ECO:0000255|HAMAP-
CC Rule:MF_01227}.
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DR EMBL; AL123456; CCP44464.1; -; Genomic_DNA.
DR PIR; B70503; B70503.
DR RefSeq; NP_216215.1; NC_000962.3.
DR RefSeq; WP_003408396.1; NZ_NVQJ01000010.1.
DR PDB; 4ZDI; X-ray; 3.52 A; A/B/C/D/E/F/G/H=1-586.
DR PDB; 4ZDJ; X-ray; 1.99 A; A=1-586.
DR PDB; 4ZDK; X-ray; 3.49 A; A/B=1-586.
DR PDBsum; 4ZDI; -.
DR PDBsum; 4ZDJ; -.
DR PDBsum; 4ZDK; -.
DR AlphaFoldDB; P9WHK7; -.
DR SMR; P9WHK7; -.
DR STRING; 83332.Rv1699; -.
DR PaxDb; P9WHK7; -.
DR DNASU; 885048; -.
DR GeneID; 45425668; -.
DR GeneID; 885048; -.
DR KEGG; mtu:Rv1699; -.
DR TubercuList; Rv1699; -.
DR eggNOG; COG0504; Bacteria.
DR OMA; EFNNAYR; -.
DR PhylomeDB; P9WHK7; -.
DR SABIO-RK; P9WHK7; -.
DR UniPathway; UPA00159; UER00277.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003883; F:CTP synthase activity; IBA:GO_Central.
DR GO; GO:0004359; F:glutaminase activity; IEA:RHEA.
DR GO; GO:0042802; F:identical protein binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0044210; P:'de novo' CTP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006241; P:CTP biosynthetic process; IBA:GO_Central.
DR GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0019856; P:pyrimidine nucleobase biosynthetic process; IBA:GO_Central.
DR CDD; cd03113; CTPS_N; 1.
DR CDD; cd01746; GATase1_CTP_Synthase; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR Gene3D; 3.40.50.880; -; 1.
DR HAMAP; MF_01227; PyrG; 1.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR004468; CTP_synthase.
DR InterPro; IPR017456; CTP_synthase_N.
DR InterPro; IPR017926; GATASE.
DR InterPro; IPR033828; GATase1_CTP_Synthase.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR11550; PTHR11550; 1.
DR Pfam; PF06418; CTP_synth_N; 1.
DR Pfam; PF00117; GATase; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00337; PyrG; 1.
DR PROSITE; PS51273; GATASE_TYPE_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Glutamine amidotransferase; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding; Pyrimidine biosynthesis;
KW Reference proteome.
FT CHAIN 1..586
FT /note="CTP synthase"
FT /id="PRO_0000138202"
FT DOMAIN 303..551
FT /note="Glutamine amidotransferase type-1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT REGION 1..278
FT /note="Amidoligase domain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT REGION 560..586
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 393
FT /note="Nucleophile; for glutamine hydrolysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227,
FT ECO:0000269|PubMed:26097035"
FT ACT_SITE 524
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227,
FT ECO:0000305|PubMed:26097035"
FT ACT_SITE 526
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227,
FT ECO:0000305|PubMed:26097035"
FT BINDING 20
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /ligand_note="allosteric inhibitor"
FT /evidence="ECO:0000250|UniProtKB:P0A7E5,
FT ECO:0000305|PubMed:26097035"
FT BINDING 20
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000305|PubMed:26097035"
FT BINDING 21..26
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26097035"
FT BINDING 46
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26097035"
FT BINDING 78
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26097035"
FT BINDING 78
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 152
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 159..161
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /ligand_note="allosteric inhibitor"
FT /evidence="ECO:0000250|UniProtKB:P0A7E5,
FT ECO:0000305|PubMed:26097035"
FT BINDING 199..204
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /ligand_note="allosteric inhibitor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 199..204
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 235
FT /ligand="CTP"
FT /ligand_id="ChEBI:CHEBI:37563"
FT /ligand_note="allosteric inhibitor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 235
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 253
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26097035"
FT BINDING 366
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 394..397
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 416
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT BINDING 477
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01227"
FT MUTAGEN 186
FT /note="V->G: 14-fold reduction in catalytic activity. 10-
FT fold decrease in affinity for ATP but no change in affinity
FT for UTP. Causes resistance to the anti-tubercular compounds
FT 7947882 and 7904688. Catalytic activity cannot be inhibited
FT by the active metabolite of 7947882."
FT /evidence="ECO:0000269|PubMed:26097035"
FT STRAND 10..16
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:4ZDK"
FT HELIX 24..37
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:4ZDK"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:4ZDK"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 98..110
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT TURN 111..116
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 121..135
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 147..153
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 163..176
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT TURN 178..180
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 181..188
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT TURN 193..196
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 201..212
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 218..226
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 247..251
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 259..265
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 268..275
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 286..296
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 299..309
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 314..317
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 318..330
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 333..341
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 342..345
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 348..355
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 373..385
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 389..392
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 394..406
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT TURN 415..417
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 424..428
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 447..455
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 460..465
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 467..480
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 482..484
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 485..488
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 489..491
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 494..498
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 504..509
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT TURN 512..514
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT STRAND 518..523
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 525..528
FT /evidence="ECO:0007829|PDB:4ZDJ"
FT HELIX 536..551
FT /evidence="ECO:0007829|PDB:4ZDJ"
SQ SEQUENCE 586 AA; 63635 MW; B49F607F9DC47E43 CRC64;
MRKHPQTATK HLFVSGGVAS SLGKGLTASS LGQLLTARGL HVTMQKLDPY LNVDPGTMNP
FQHGEVFVTE DGAETDLDVG HYERFLDRNL PGSANVTTGQ VYSTVIAKER RGEYLGDTVQ
VIPHITDEIK RRILAMAQPD ADGNRPDVVI TEIGGTVGDI ESQPFLEAAR QVRHYLGRED
VFFLHVSLVP YLAPSGELKT KPTQHSVAAL RSIGITPDAL ILRCDRDVPE ALKNKIALMC
DVDIDGVIST PDAPSIYDIP KVLHREELDA FVVRRLNLPF RDVDWTEWDD LLRRVHEPHE
TVRIALVGKY VELSDAYLSV AEALRAGGFK HRAKVEICWV ASDGCETTSG AAAALGDVHG
VLIPGGFGIR GIEGKIGAIA YARARGLPVL GLCLGLQCIV IEAARSVGLT NANSAEFDPD
TPDPVIATMP DQEEIVAGEA DLGGTMRLGS YPAVLEPDSV VAQAYQTTQV SERHRHRYEV
NNAYRDKIAE SGLRFSGTSP DGHLVEFVEY PPDRHPFVVG TQAHPELKSR PTRPHPLFVA
FVGAAIDYKA GELLPVEIPE IPEHTPNGSS HRDGVGQPLP EPASRG
