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Inosine-5'-monophosphate dehydrogenase (IMP dehydrogenase) (IMPD) (IMPDH) (EC 1.1.1.205) (IMPDH2)

 IMDH_MYCTU              Reviewed;         529 AA.
P9WKI7; L0TCG3; P65167; Q50715;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
10-OCT-2018, entry version 29.
RecName: Full=Inosine-5'-monophosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01964};
Short=IMP dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01964};
Short=IMPD {ECO:0000255|HAMAP-Rule:MF_01964};
Short=IMPDH {ECO:0000255|HAMAP-Rule:MF_01964};
EC=1.1.1.205 {ECO:0000255|HAMAP-Rule:MF_01964, ECO:0000269|PubMed:20491506, ECO:0000269|PubMed:21081761};
AltName: Full=IMPDH2 {ECO:0000303|PubMed:26440283};
Name=guaB {ECO:0000255|HAMAP-Rule:MF_01964};
Synonyms=guaB2 {ECO:0000303|PubMed:20491506,
ECO:0000303|PubMed:21081761, ECO:0000312|EMBL:CCP46233.1};
OrderedLocusNames=Rv3411c; ORFNames=MTCY78.17;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=12657046; DOI=10.1046/j.1365-2958.2003.03425.x;
Sassetti C.M., Boyd D.H., Rubin E.J.;
"Genes required for mycobacterial growth defined by high density
mutagenesis.";
Mol. Microbiol. 48:77-84(2003).
[3]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
ACTIVITY REGULATION.
STRAIN=H37Rv;
PubMed=20491506; DOI=10.1021/jm100424m;
Chen L., Wilson D.J., Xu Y., Aldrich C.C., Felczak K., Sham Y.Y.,
Pankiewicz K.W.;
"Triazole-linked inhibitors of inosine monophosphate dehydrogenase
from human and Mycobacterium tuberculosis.";
J. Med. Chem. 53:4768-4778(2010).
[4]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
AND ACTIVITY REGULATION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=21081761; DOI=10.1099/mic.0.042549-0;
Usha V., Gurcha S.S., Lovering A.L., Lloyd A.J., Papaemmanouil A.,
Reynolds R.C., Besra G.S.;
"Identification of novel diphenyl urea inhibitors of Mt-GuaB2 active
against Mycobacterium tuberculosis.";
Microbiology 157:290-299(2011).
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[6]
ACTIVITY REGULATION.
STRAIN=H37Rv;
PubMed=22479467; DOI=10.1371/journal.pone.0033886;
Usha V., Hobrath J.V., Gurcha S.S., Reynolds R.C., Besra G.S.;
"Identification of novel Mt-Guab2 inhibitor series active against M.
tuberculosis.";
PLoS ONE 7:E33886-E33886(2012).
[7]
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 1-125 AND 253-529 IN
COMPLEXES WITH POTASSIUM; XMP; NAD(+); IMP AND INHIBITORS WITH
ANTITUBERCULAR ACTIVITY, ACTIVITY REGULATION, REACTION MECHANISM,
ACTIVE SITE, AND SUBUNIT.
STRAIN=H37Rv;
PubMed=26440283; DOI=10.1371/journal.pone.0138976;
Makowska-Grzyska M., Kim Y., Gorla S.K., Wei Y., Mandapati K.,
Zhang M., Maltseva N., Modi G., Boshoff H.I., Gu M., Aldrich C.,
Cuny G.D., Hedstrom L., Joachimiak A.;
"Mycobacterium tuberculosis IMPDH in complexes with substrates,
products and antitubercular compounds.";
PLoS ONE 10:E0138976-E0138976(2015).
-!- FUNCTION: Catalyzes the conversion of inosine 5'-phosphate (IMP)
to xanthosine 5'-phosphate (XMP), the first committed and rate-
limiting step in the de novo synthesis of guanine nucleotides, and
therefore plays an important role in the regulation of cell growth
(PubMed:20491506, PubMed:21081761). Does not catalyze the reverse
reaction, i.e. the conversion of XMP to IMP (PubMed:21081761).
Appears to be essential for the optimal growth of M.tuberculosis
(PubMed:12657046). {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:12657046, ECO:0000269|PubMed:20491506,
ECO:0000269|PubMed:21081761}.
-!- CATALYTIC ACTIVITY: Inosine 5'-phosphate + NAD(+) + H(2)O =
xanthosine 5'-phosphate + NADH. {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:20491506, ECO:0000269|PubMed:21081761}.
-!- COFACTOR:
Name=K(+); Xref=ChEBI:CHEBI:29103;
Evidence={ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:21081761};
-!- ACTIVITY REGULATION: Mycophenolic acid (MPA) is a non-competitive
inhibitor that prevents formation of the closed enzyme
conformation by binding to the same site as the amobile flap. In
contrast, mizoribine monophosphate (MZP) is a competitive
inhibitor that induces the closed conformation. MPA is a potent
inhibitor of mammalian IMPDHs but a poor inhibitor of the
bacterial enzymes. MZP is a more potent inhibitor of bacterial
IMPDH (By similarity). Inhibited by the products XMP and NADH.
Significantly inhibited in vitro by a panel of diphenyl urea-based
derivatives and a series of novel classes of inhibitors, which are
also potent anti-mycobacterial agents against M.tuberculosis and
M.smegmatis (PubMed:21081761) (PubMed:22479467). Is also inhibited
by a mycophenolic adenine dinucleotide (MAD) derivative in which a
1,2,3-triazole linker was incorporated as isosteric replacement of
the pyrophosphate linker, thereby mimicking NAD (PubMed:20491506).
Other inhibitors with modular structures consisting of two
aromatic moieties connected by different linkers (such as urea and
amide) have been identified and shown to exhibit antitubercular
activity (PubMed:26440283). {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:20491506, ECO:0000269|PubMed:21081761,
ECO:0000269|PubMed:22479467, ECO:0000269|PubMed:26440283}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=78 uM for inosine 5'-phosphate {ECO:0000269|PubMed:20491506};
KM=1005 uM for NAD(+) {ECO:0000269|PubMed:20491506};
KM=128.1 uM for inosine 5'-phosphate
{ECO:0000269|PubMed:21081761};
KM=610.5 uM for NAD(+) {ECO:0000269|PubMed:21081761};
Note=kcat is 0.53 sec(-1). {ECO:0000269|PubMed:20491506};
pH dependence:
Optimum pH is 8-8.5. {ECO:0000269|PubMed:21081761};
Temperature dependence:
Optimum temperature is 37 degrees Celsius.
{ECO:0000269|PubMed:21081761};
-!- PATHWAY: Purine metabolism; XMP biosynthesis via de novo pathway;
XMP from IMP: step 1/1. {ECO:0000255|HAMAP-Rule:MF_01964}.
-!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000305|PubMed:26440283}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene display impaired
growth. {ECO:0000269|PubMed:12657046}.
-!- SIMILARITY: Belongs to the IMPDH/GMPR family. {ECO:0000255|HAMAP-
Rule:MF_01964}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP46233.1; -; Genomic_DNA.
PIR; H70736; H70736.
RefSeq; NP_217928.1; NC_000962.3.
RefSeq; WP_003900682.1; NZ_KK339370.1.
PDB; 4ZQM; X-ray; 1.60 A; A=1-125, A=253-529.
PDB; 4ZQN; X-ray; 2.00 A; A=1-125, A=253-529.
PDB; 4ZQO; X-ray; 1.76 A; A=1-125, A=253-529.
PDB; 4ZQP; X-ray; 1.90 A; A=1-125, A=253-529.
PDB; 4ZQR; X-ray; 1.69 A; A/B/C/D=1-125, A/B/C/D=253-529.
PDB; 5UPU; X-ray; 2.90 A; A=1-125, A=256-529.
PDB; 5UPV; X-ray; 1.63 A; A=1-125, A=256-529.
PDBsum; 4ZQM; -.
PDBsum; 4ZQN; -.
PDBsum; 4ZQO; -.
PDBsum; 4ZQP; -.
PDBsum; 4ZQR; -.
PDBsum; 5UPU; -.
PDBsum; 5UPV; -.
ProteinModelPortal; P9WKI7; -.
SMR; P9WKI7; -.
STRING; 83332.Rv3411c; -.
PaxDb; P9WKI7; -.
PRIDE; P9WKI7; -.
EnsemblBacteria; CCP46233; CCP46233; Rv3411c.
GeneID; 887498; -.
KEGG; mtu:Rv3411c; -.
TubercuList; Rv3411c; -.
eggNOG; ENOG4105CP4; Bacteria.
eggNOG; COG0516; LUCA.
eggNOG; COG0517; LUCA.
KO; K00088; -.
OMA; GIGIVHK; -.
PhylomeDB; P9WKI7; -.
UniPathway; UPA00601; UER00295.
Proteomes; UP000001584; Chromosome.
GO; GO:0005618; C:cell wall; IDA:MTBBASE.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0003938; F:IMP dehydrogenase activity; IDA:MTBBASE.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-UniRule.
GO; GO:0006177; P:GMP biosynthetic process; IDA:MTBBASE.
GO; GO:0006183; P:GTP biosynthetic process; IBA:GO_Central.
GO; GO:0006204; P:IMP catabolic process; IDA:MTBBASE.
GO; GO:0097293; P:XMP biosynthetic process; IDA:MTBBASE.
CDD; cd00381; IMPDH; 1.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_01964; IMPDH; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR000644; CBS_dom.
InterPro; IPR005990; IMP_DH.
InterPro; IPR015875; IMP_DH/GMP_Rdtase_CS.
InterPro; IPR001093; IMP_DH_GMPRt.
Pfam; PF00571; CBS; 2.
Pfam; PF00478; IMPDH; 1.
PIRSF; PIRSF000130; IMPDH; 1.
SMART; SM00116; CBS; 2.
TIGRFAMs; TIGR01302; IMP_dehydrog; 1.
PROSITE; PS51371; CBS; 2.
PROSITE; PS00487; IMP_DH_GMP_RED; 1.
1: Evidence at protein level;
3D-structure; CBS domain; Complete proteome; GMP biosynthesis;
Metal-binding; NAD; Oxidoreductase; Potassium; Purine biosynthesis;
Reference proteome; Repeat.
CHAIN 1 529 Inosine-5'-monophosphate dehydrogenase.
/FTId=PRO_0000093702.
DOMAIN 129 185 CBS 1. {ECO:0000255|HAMAP-Rule:MF_01964}.
DOMAIN 189 246 CBS 2. {ECO:0000255|HAMAP-Rule:MF_01964}.
NP_BIND 334 336 NAD. {ECO:0000255|HAMAP-Rule:MF_01964}.
REGION 374 376 IMP binding. {ECO:0000255|HAMAP-
Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
REGION 397 398 IMP binding. {ECO:0000255|HAMAP-
Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
REGION 421 425 IMP binding. {ECO:0000255|HAMAP-
Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
ACT_SITE 341 341 Thioimidate intermediate.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000305|PubMed:26440283}.
ACT_SITE 443 443 Proton acceptor. {ECO:0000255|HAMAP-
Rule:MF_01964,
ECO:0000305|PubMed:26440283}.
METAL 336 336 Potassium; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
METAL 338 338 Potassium; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
METAL 341 341 Potassium; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
METAL 511 511 Potassium; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
METAL 512 512 Potassium; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
METAL 513 513 Potassium; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
BINDING 283 283 NAD. {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
BINDING 289 289 NAD. {ECO:0000269|PubMed:26440283}.
BINDING 339 339 IMP. {ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
BINDING 343 343 NAD. {ECO:0000269|PubMed:26440283}.
BINDING 458 458 IMP; via carbonyl oxygen.
{ECO:0000255|HAMAP-Rule:MF_01964,
ECO:0000269|PubMed:26440283}.
BINDING 458 458 NAD. {ECO:0000269|PubMed:26440283}.
STRAND 33 35 {ECO:0000244|PDB:4ZQM}.
STRAND 39 44 {ECO:0000244|PDB:4ZQR}.
HELIX 47 49 {ECO:0000244|PDB:4ZQM}.
STRAND 50 52 {ECO:0000244|PDB:4ZQM}.
HELIX 61 63 {ECO:0000244|PDB:4ZQM}.
STRAND 68 73 {ECO:0000244|PDB:4ZQM}.
STRAND 75 78 {ECO:0000244|PDB:4ZQM}.
STRAND 80 82 {ECO:0000244|PDB:4ZQM}.
TURN 86 88 {ECO:0000244|PDB:4ZQM}.
HELIX 91 99 {ECO:0000244|PDB:4ZQM}.
STRAND 102 106 {ECO:0000244|PDB:4ZQM}.
STRAND 108 110 {ECO:0000244|PDB:4ZQM}.
HELIX 112 123 {ECO:0000244|PDB:4ZQM}.
STRAND 256 259 {ECO:0000244|PDB:4ZQM}.
HELIX 263 274 {ECO:0000244|PDB:4ZQM}.
STRAND 278 283 {ECO:0000244|PDB:4ZQM}.
HELIX 290 303 {ECO:0000244|PDB:4ZQM}.
TURN 304 306 {ECO:0000244|PDB:4ZQM}.
STRAND 307 314 {ECO:0000244|PDB:4ZQM}.
HELIX 317 326 {ECO:0000244|PDB:4ZQM}.
STRAND 329 333 {ECO:0000244|PDB:4ZQM}.
HELIX 343 346 {ECO:0000244|PDB:4ZQM}.
HELIX 353 364 {ECO:0000244|PDB:4ZQM}.
HELIX 365 367 {ECO:0000244|PDB:4ZQM}.
STRAND 371 375 {ECO:0000244|PDB:4ZQM}.
HELIX 380 388 {ECO:0000244|PDB:4ZQM}.
STRAND 392 397 {ECO:0000244|PDB:4ZQM}.
HELIX 398 401 {ECO:0000244|PDB:4ZQM}.
STRAND 406 408 {ECO:0000244|PDB:4ZQM}.
STRAND 411 413 {ECO:0000244|PDB:4ZQM}.
STRAND 416 422 {ECO:0000244|PDB:4ZQM}.
TURN 427 429 {ECO:0000244|PDB:4ZQM}.
STRAND 461 465 {ECO:0000244|PDB:4ZQM}.
HELIX 470 488 {ECO:0000244|PDB:4ZQM}.
HELIX 493 496 {ECO:0000244|PDB:4ZQM}.
STRAND 501 503 {ECO:0000244|PDB:4ZQM}.
HELIX 506 508 {ECO:0000244|PDB:4ZQM}.
STRAND 516 521 {ECO:0000244|PDB:4ZQR}.
SEQUENCE 529 AA; 54867 MW; 689A7C7C53993C0A CRC64;
MSRGMSGLED SSDLVVSPYV RMGGLTTDPV PTGGDDPHKV AMLGLTFDDV LLLPAASDVV
PATADTSSQL TKKIRLKVPL VSSAMDTVTE SRMAIAMARA GGMGVLHRNL PVAEQAGQVE
MVKRSEAGMV TDPVTCRPDN TLAQVDALCA RFRISGLPVV DDDGALVGII TNRDMRFEVD
QSKQVAEVMT KAPLITAQEG VSASAALGLL RRNKIEKLPV VDGRGRLTGL ITVKDFVKTE
QHPLATKDSD GRLLVGAAVG VGGDAWVRAM MLVDAGVDVL VVDTAHAHNR LVLDMVGKLK
SEVGDRVEVV GGNVATRSAA AALVDAGADA VKVGVGPGSI CTTRVVAGVG APQITAILEA
VAACRPAGVP VIADGGLQYS GDIAKALAAG ASTAMLGSLL AGTAEAPGEL IFVNGKQYKS
YRGMGSLGAM RGRGGATSYS KDRYFADDAL SEDKLVPEGI EGRVPFRGPL SSVIHQLTGG
LRAAMGYTGS PTIEVLQQAQ FVRITPAGLK ESHPHDVAMT VEAPNYYAR


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