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

 IMDH_TRIFO              Reviewed;         503 AA.
P50097;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 1.
23-MAY-2018, entry version 125.
RecName: Full=Inosine-5'-monophosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_03156};
Short=IMP dehydrogenase {ECO:0000255|HAMAP-Rule:MF_03156};
Short=IMPD {ECO:0000255|HAMAP-Rule:MF_03156};
Short=IMPDH {ECO:0000255|HAMAP-Rule:MF_03156};
EC=1.1.1.205 {ECO:0000255|HAMAP-Rule:MF_03156};
Name=IMPDH {ECO:0000255|HAMAP-Rule:MF_03156};
Tritrichomonas foetus (Trichomonas foetus) (Tritrichomonas suis).
Eukaryota; Parabasalia; Tritrichomonadida; Tritrichomonadidae;
Tritrichomonas.
NCBI_TaxID=56690;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=UNK;
PubMed=7905423; DOI=10.1006/expr.1994.1010;
Beck J.T., Zhao S., Wang C.C.;
"Cloning, sequencing, and structural analysis of the DNA encoding
inosine monophosphate dehydrogenase (EC 1.1.1.205) from Tritrichomonas
foetus.";
Exp. Parasitol. 78:101-112(1994).
[2]
SEQUENCE REVISION.
Wang C.C.;
Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
[3]
ENZYME REGULATION.
PubMed=1967525; DOI=10.1016/0006-2952(90)90659-9;
Hedstrom L., Cheung K.S., Wang C.C.;
"A novel mechanism of mycophenolic acid resistance in the protozoan
parasite Tritrichomonas foetus.";
Biochem. Pharmacol. 39:151-160(1990).
[4]
CHARACTERIZATION.
PubMed=7577983; DOI=10.1021/bi00042a021;
Huete-Perez J.A., Wu J.C., Whitby F.G., Wang C.C.;
"Identification of the IMP binding site in the IMP dehydrogenase from
Tritrichomonas foetus.";
Biochemistry 34:13889-13894(1995).
[5]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF CYS-319.
PubMed=10029522; DOI=10.1021/bi982305k;
Digits J.A., Hedstrom L.;
"Kinetic mechanism of Tritrichomonas foetus inosine 5'-monophosphate
dehydrogenase.";
Biochemistry 38:2295-2306(1999).
[6]
NUCLEIC ACID-BINDING.
PubMed=14766016; DOI=10.1042/BJ20031585;
McLean J.E., Hamaguchi N., Belenky P., Mortimer S.E., Stanton M.,
Hedstrom L.;
"Inosine 5'-monophosphate dehydrogenase binds nucleic acids in vitro
and in vivo.";
Biochem. J. 379:243-251(2004).
[7]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
PubMed=9271497; DOI=10.1021/bi9708850;
Whitby F.G., Luecke H., Kuhn P., Somoza J.R., Huete-Perez J.A.,
Phillips J.D., Hill C.P., Fletterick R.J., Wang C.C.;
"Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate
dehydrogenase and the enzyme-product complex.";
Biochemistry 36:10666-10674(1997).
[8]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 4-377 IN COMPLEX WITH
SUBSTRATE AND INHIBITOR, AND POTASSIUM-BINDING.
PubMed=12403633; DOI=10.1021/bi0203785;
Gan L., Petsko G.A., Hedstrom L.;
"Crystal structure of a ternary complex of Tritrichomonas foetus
inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site
loop for catalysis.";
Biochemistry 41:13309-13317(2002).
[9]
X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH INHIBITOR, AND
ACTIVE SITE.
PubMed=12235158; DOI=10.1074/jbc.M208330200;
Prosise G.L., Wu J.Z., Luecke H.;
"Crystal structure of Tritrichomonas foetus inosine monophosphate
dehydrogenase in complex with the inhibitor ribavirin monophosphate
reveals a catalysis-dependent ion-binding site.";
J. Biol. Chem. 277:50654-50659(2002).
[10]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 4-377 IN COMPLEX WITH
INHIBITOR (MIZORIBINE MONOPHOSPHATE; MZP) AND POTASSIUM, AND ACTIVE
SITE.
PubMed=12549902; DOI=10.1021/bi0271401;
Gan L., Seyedsayamdost M.R., Shuto S., Matsuda A., Petsko G.A.,
Hedstrom L.;
"The immunosuppressive agent mizoribine monophosphate forms a
transition state analogue complex with inosine monophosphate
dehydrogenase.";
Biochemistry 42:857-863(2003).
[11]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-483 IN COMPLEX WITH
SUBSTRATE; PRODUCT; INHIBITOR (MYCOPHENOLIC ACID; MPA) AND NAD(+).
PubMed=12559919; DOI=10.1016/S0022-2836(02)01383-9;
Prosise G.L., Luecke H.;
"Crystal structures of Tritrichomonas foetus inosine monophosphate
dehydrogenase in complex with substrate, cofactor and analogs: a
structural basis for the random-in ordered-out kinetic mechanism.";
J. Mol. Biol. 326:517-527(2003).
-!- 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. Could also have a single-stranded nucleic acid-binding
activity and could play a role in RNA and/or DNA metabolism.
{ECO:0000255|HAMAP-Rule:MF_03156, ECO:0000269|PubMed:10029522}.
-!- CATALYTIC ACTIVITY: Inosine 5'-phosphate + NAD(+) + H(2)O =
xanthosine 5'-phosphate + NADH. {ECO:0000255|HAMAP-Rule:MF_03156}.
-!- COFACTOR:
Name=K(+); Xref=ChEBI:CHEBI:29103;
Evidence={ECO:0000255|HAMAP-Rule:MF_03156};
-!- ENZYME 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. {ECO:0000255|HAMAP-Rule:MF_03156,
ECO:0000269|PubMed:1967525}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.7 uM for Inosine 5'-phosphate
{ECO:0000269|PubMed:10029522};
KM=150 uM for NAD(+) {ECO:0000269|PubMed:10029522};
-!- PATHWAY: Purine metabolism; XMP biosynthesis via de novo pathway;
XMP from IMP: step 1/1. {ECO:0000255|HAMAP-Rule:MF_03156}.
-!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_03156,
ECO:0000269|PubMed:12235158, ECO:0000269|PubMed:12403633,
ECO:0000269|PubMed:12549902, ECO:0000269|PubMed:12559919}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03156}.
-!- MISCELLANEOUS: Contains 2 potassium ions bound at each subunit
interface. The second potassium binding site is not conserved and
not observed in crystal structures of IMPDHs from other organisms
(PubMed:12403633). {ECO:0000305|PubMed:12403633}.
-!- SIMILARITY: Belongs to the IMPDH/GMPR family. {ECO:0000255|HAMAP-
Rule:MF_03156}.
-----------------------------------------------------------------------
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EMBL; L18917; AAB01581.1; -; Genomic_DNA.
PIR; A58910; A58910.
PDB; 1AK5; X-ray; 2.30 A; A=1-503.
PDB; 1LRT; X-ray; 2.20 A; A/B/C/D=2-503.
PDB; 1ME7; X-ray; 2.15 A; A=1-503.
PDB; 1ME8; X-ray; 1.90 A; A=1-503.
PDB; 1ME9; X-ray; 2.20 A; A=1-503.
PDB; 1MEH; X-ray; 1.95 A; A=1-503.
PDB; 1MEI; X-ray; 2.20 A; A=1-503.
PDB; 1MEW; X-ray; 2.15 A; A=1-503.
PDB; 1PVN; X-ray; 2.00 A; A/B/C/D=2-503.
PDBsum; 1AK5; -.
PDBsum; 1LRT; -.
PDBsum; 1ME7; -.
PDBsum; 1ME8; -.
PDBsum; 1ME9; -.
PDBsum; 1MEH; -.
PDBsum; 1MEI; -.
PDBsum; 1MEW; -.
PDBsum; 1PVN; -.
DisProt; DP00399; -.
ProteinModelPortal; P50097; -.
SMR; P50097; -.
PRIDE; P50097; -.
SABIO-RK; P50097; -.
UniPathway; UPA00601; UER00295.
EvolutionaryTrace; P50097; -.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0032991; C:protein-containing complex; IDA:CAFA.
GO; GO:0042802; F:identical protein binding; IDA:CAFA.
GO; GO:0003938; F:IMP dehydrogenase activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000166; F:nucleotide binding; IDA:UniProtKB.
GO; GO:0006177; P:GMP biosynthetic process; IEA:UniProtKB-KW.
GO; GO:0051289; P:protein homotetramerization; IDA:CAFA.
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; 1.
Pfam; PF00478; IMPDH; 1.
PIRSF; PIRSF000130; IMPDH; 1.
PROSITE; PS51371; CBS; 2.
PROSITE; PS00487; IMP_DH_GMP_RED; 1.
1: Evidence at protein level;
3D-structure; CBS domain; Cytoplasm; GMP biosynthesis; Metal-binding;
NAD; Oxidoreductase; Potassium; Purine biosynthesis; Repeat.
CHAIN 1 503 Inosine-5'-monophosphate dehydrogenase.
/FTId=PRO_0000093676.
DOMAIN 103 163 CBS 1. {ECO:0000255|HAMAP-Rule:MF_03156}.
DOMAIN 167 228 CBS 2. {ECO:0000255|HAMAP-Rule:MF_03156}.
NP_BIND 261 263 NAD.
NP_BIND 312 314 NAD.
REGION 358 360 IMP binding.
REGION 381 382 IMP binding.
REGION 405 409 IMP binding.
ACT_SITE 319 319 Thioimidate intermediate.
{ECO:0000255|HAMAP-Rule:MF_03156,
ECO:0000269|PubMed:12235158,
ECO:0000269|PubMed:12549902}.
ACT_SITE 418 418 Proton acceptor. {ECO:0000255|HAMAP-
Rule:MF_03156}.
METAL 20 20 Potassium 2; via carbonyl oxygen.
{ECO:0000269|PubMed:12549902}.
METAL 22 22 Potassium 2.
{ECO:0000269|PubMed:12549902}.
METAL 264 264 Potassium 2; shared with tetrameric
partner. {ECO:0000269|PubMed:12549902}.
METAL 266 266 Potassium 2; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000269|PubMed:12549902}.
METAL 314 314 Potassium 1; via carbonyl oxygen.
{ECO:0000269|PubMed:12549902}.
METAL 316 316 Potassium 1; via carbonyl oxygen.
{ECO:0000269|PubMed:12549902}.
METAL 319 319 Potassium 1; via carbonyl oxygen.
{ECO:0000269|PubMed:12549902}.
METAL 460 460 Potassium 2; via carbonyl oxygen.
{ECO:0000269|PubMed:12549902}.
METAL 485 485 Potassium 1; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000269|PubMed:12549902}.
METAL 486 486 Potassium 1; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000269|PubMed:12549902}.
METAL 487 487 Potassium 1; via carbonyl oxygen; shared
with tetrameric partner.
{ECO:0000269|PubMed:12549902}.
BINDING 317 317 IMP.
BINDING 431 431 IMP.
MUTAGEN 319 319 C->S: Has less than 0.06% of the wild-
type activity.
{ECO:0000269|PubMed:10029522}.
HELIX 12 14 {ECO:0000244|PDB:1ME8}.
STRAND 15 17 {ECO:0000244|PDB:1ME8}.
HELIX 28 30 {ECO:0000244|PDB:1ME8}.
STRAND 49 56 {ECO:0000244|PDB:1ME8}.
TURN 60 62 {ECO:0000244|PDB:1ME8}.
HELIX 65 73 {ECO:0000244|PDB:1ME8}.
STRAND 77 80 {ECO:0000244|PDB:1ME8}.
STRAND 82 84 {ECO:0000244|PDB:1ME7}.
HELIX 86 97 {ECO:0000244|PDB:1ME8}.
TURN 98 100 {ECO:0000244|PDB:1ME8}.
STRAND 235 238 {ECO:0000244|PDB:1ME8}.
STRAND 240 242 {ECO:0000244|PDB:1ME8}.
HELIX 243 253 {ECO:0000244|PDB:1ME8}.
STRAND 256 260 {ECO:0000244|PDB:1ME8}.
HELIX 268 281 {ECO:0000244|PDB:1ME8}.
HELIX 282 284 {ECO:0000244|PDB:1ME8}.
STRAND 287 292 {ECO:0000244|PDB:1ME8}.
HELIX 295 304 {ECO:0000244|PDB:1ME8}.
STRAND 307 311 {ECO:0000244|PDB:1ME8}.
HELIX 317 321 {ECO:0000244|PDB:1MEH}.
TURN 322 325 {ECO:0000244|PDB:1ME8}.
HELIX 331 349 {ECO:0000244|PDB:1ME8}.
STRAND 350 352 {ECO:0000244|PDB:1ME8}.
STRAND 355 359 {ECO:0000244|PDB:1ME8}.
HELIX 364 372 {ECO:0000244|PDB:1ME8}.
STRAND 376 381 {ECO:0000244|PDB:1ME8}.
HELIX 382 385 {ECO:0000244|PDB:1ME8}.
STRAND 390 392 {ECO:0000244|PDB:1ME8}.
STRAND 394 397 {ECO:0000244|PDB:1ME8}.
STRAND 400 406 {ECO:0000244|PDB:1ME8}.
HELIX 411 414 {ECO:0000244|PDB:1ME8}.
HELIX 416 419 {ECO:0000244|PDB:1PVN}.
STRAND 421 423 {ECO:0000244|PDB:1PVN}.
STRAND 434 438 {ECO:0000244|PDB:1ME8}.
HELIX 443 460 {ECO:0000244|PDB:1ME8}.
HELIX 466 472 {ECO:0000244|PDB:1ME8}.
STRAND 475 477 {ECO:0000244|PDB:1ME8}.
TURN 480 482 {ECO:0000244|PDB:1MEH}.
TURN 484 486 {ECO:0000244|PDB:1ME8}.
STRAND 490 493 {ECO:0000244|PDB:1PVN}.
SEQUENCE 503 AA; 55473 MW; E204EADE7ECC4134 CRC64;
MAKYYNEPCH TFNEYLLIPG LSTVDCIPSN VNLSTPLVKF QKGQQSEINL KIPLVSAIMQ
SVSGEKMAIA LAREGGISFI FGSQSIESQA AMVHAVKNFK AGFVVSDSNV KPDQTFADVL
AISQRTTHNT VAVTDDGTPH GVLLGLVTQR DYPIDLTQTE TKVSDMMTPF SKLVTAHQDT
KLSEANKIIW EKKLNALPII DDDQHLRYIV FRKDYDRSQV CHNELVDSQK RYLVGAGINT
RDFRERVPAL VEAGADVLCI DSSDGFSEWQ KITIGWIREK YGDKVKVGAG NIVDGEGFRY
LADAGADFIK IGIGGGSICI TREQKGIGRG QATAVIDVVA ERNKYFEETG IYIPVCSDGG
IVYDYHMTLA LAMGADFIML GRYFARFEES PTRKVTINGS VMKEYWGEGS SRARNWQRYD
LGGKQKLSFE EGVDSYVPYA GKLKDNVEAS LNKVKSTMCN CGALTIPQLQ SKAKITLVSS
VSIVEGGAHD VIVKDRINDY HPK


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