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Protein

Inosine-5'-monophosphate dehydrogenase 2

Gene

IMD2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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. In contrast to the other IMPDH alleles IMD3 and IMD4, the enzymatic activity of IMD2 seems to be intrinsically drug resistant.UniRule annotation3 Publications

Catalytic activityi

Inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH.UniRule annotation

Cofactori

K+UniRule annotation

Enzyme regulationi

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.UniRule annotation

Pathwayi: XMP biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes XMP from IMP.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Inosine-5'-monophosphate dehydrogenase 2 (IMD2), Inosine-5'-monophosphate dehydrogenase 3 (IMD3), Inosine-5'-monophosphate dehydrogenase 4 (IMD4), Putative inosine-5'-monophosphate dehydrogenase 1 (IMD1)
This subpathway is part of the pathway XMP biosynthesis via de novo pathway, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes XMP from IMP, the pathway XMP biosynthesis via de novo pathway and in Purine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi330Potassium; via carbonyl oxygenUniRule annotation1
Metal bindingi332Potassium; via carbonyl oxygenUniRule annotation1
Binding sitei333IMPUniRule annotation1
Active sitei335Thioimidate intermediateUniRule annotation1
Metal bindingi335Potassium; via carbonyl oxygenUniRule annotation1
Active sitei437Proton acceptorUniRule annotation1
Binding sitei449IMPUniRule annotation1
Metal bindingi508Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation1
Metal bindingi509Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation1
Metal bindingi510Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi278 – 280NADUniRule annotation3
Nucleotide bindingi328 – 330NADUniRule annotation3

GO - Molecular functioni

  • chromatin binding Source: SGD
  • IMP dehydrogenase activity Source: SGD
  • metal ion binding Source: UniProtKB-HAMAP
  • nucleotide binding Source: UniProtKB-HAMAP

GO - Biological processi

  • GMP biosynthetic process Source: UniProtKB-HAMAP
  • GTP biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

GMP biosynthesis, Purine biosynthesis

Keywords - Ligandi

Metal-binding, NAD, Potassium

Enzyme and pathway databases

BioCyciYEAST:YHR216W-MONOMER.
ReactomeiR-SCE-6798695. Neutrophil degranulation.
R-SCE-73817. Purine ribonucleoside monophosphate biosynthesis.
R-SCE-74217. Purine salvage.
SABIO-RKP38697.
UniPathwayiUPA00601; UER00295.

Names & Taxonomyi

Protein namesi
Recommended name:
Inosine-5'-monophosphate dehydrogenase 2UniRule annotation (EC:1.1.1.205UniRule annotation)
Short name:
IMP dehydrogenase 2UniRule annotation
Short name:
IMPD 2UniRule annotation
Short name:
IMPDH 2UniRule annotation
Gene namesi
Name:IMD2UniRule annotation
Synonyms:PUR5
Ordered Locus Names:YHR216W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VIII

Organism-specific databases

EuPathDBiFungiDB:YHR216W.
SGDiS000001259. IMD2.

Subcellular locationi

GO - Cellular componenti

  • chromatin Source: SGD
  • cytoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi253S → A: Reduces drug-resistance to MPA. 1 Publication1
Mutagenesisi335C → A: Inactivates the proteins ability to provide drug-resistance in vivo. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000936821 – 523Inosine-5'-monophosphate dehydrogenase 2Add BLAST523

Proteomic databases

MaxQBiP38697.
PRIDEiP38697.

Expressioni

Inductioni

Induced by MPA resulting in resistance to the drug. Repressed by nutrient limitation.1 Publication

Interactioni

Subunit structurei

Homotetramer. Seems to be able to form heterotetramers composed from more than 1 of the 3 IMPDH gene products (IMD2-4).UniRule annotation1 Publication

Protein-protein interaction databases

BioGridi36651. 62 interactors.
DIPiDIP-2840N.
IntActiP38697. 39 interactors.
MINTiMINT-521280.

Structurei

3D structure databases

ProteinModelPortaliP38697.
SMRiP38697.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini121 – 183CBS 1UniRule annotationAdd BLAST63
Domaini184 – 240CBS 2UniRule annotationAdd BLAST57

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni368 – 370IMP bindingUniRule annotation3
Regioni391 – 392IMP bindingUniRule annotation2
Regioni415 – 419IMP bindingUniRule annotation5

Sequence similaritiesi

Belongs to the IMPDH/GMPR family.UniRule annotation
Contains 2 CBS domains.UniRule annotation

Keywords - Domaini

CBS domain, Repeat

Phylogenomic databases

GeneTreeiENSGT00530000062923.
HOGENOMiHOG000165752.
KOiK00088.
OMAiRYFIESE.
OrthoDBiEOG092C1U8P.

Family and domain databases

CDDicd00381. IMPDH. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01964. IMPDH. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR000644. CBS_dom.
IPR005990. IMP_DH.
IPR015875. IMP_DH/GMP_Rdtase_CS.
IPR001093. IMP_DH_GMPRt.
[Graphical view]
PANTHERiPTHR11911:SF6. PTHR11911:SF6. 2 hits.
PfamiPF00571. CBS. 2 hits.
PF00478. IMPDH. 1 hit.
[Graphical view]
PIRSFiPIRSF000130. IMPDH. 1 hit.
SMARTiSM00116. CBS. 2 hits.
[Graphical view]
TIGRFAMsiTIGR01302. IMP_dehydrog. 1 hit.
PROSITEiPS51371. CBS. 2 hits.
PS00487. IMP_DH_GMP_RED. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38697-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAIRDYKTA LDFTKSLPRP DGLSVQELMD SKIRGGLTYN DFLILPGLVD
60 70 80 90 100
FASSEVSLQT KLTRNITLNI PLVSSPMDTV TESEMATFMA LLGGIGFIHH
110 120 130 140 150
NCTPEDQADM VRRVKNYENG FINNPIVISP TTTVGEAKSM KEKYGFAGFP
160 170 180 190 200
VTTDGKRNAK LVGVITSRDI QFVEDNSLLV QDVMTKNPVT GAQGITLSEG
210 220 230 240 250
NEILKKIKKG RLLVVDEKGN LVSMLSRTDL MKNQNYPLAS KSANTKQLLC
260 270 280 290 300
GASIGTMDAD KERLRLLVKA GLDVVILDSS QGNSIFELNM LKWVKESFPG
310 320 330 340 350
LEVIAGNVVT REQAANLIAA GADGLRIGMG TGSICITQEV MACGRPQGTA
360 370 380 390 400
VYNVCEFANQ FGVPCMADGG VQNIGHITKA LALGSSTVMM GGMLAGTTES
410 420 430 440 450
PGEYFYQDGK RLKAYRGMGS IDAMQKTGTK GNASTSRYFS ESDSVLVAQG
460 470 480 490 500
VSGAVVDKGS IKKFIPYLYN GLQHSCQDIG CRSLTLLKNN VQRGKVRFEF
510 520
RTASAQLEGG VHNLHSYEKR LHN
Length:523
Mass (Da):56,530
Last modified:February 1, 1995 - v1
Checksum:i7CA3EC11238906B9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00029 Genomic DNA. Translation: AAB69728.1.
BK006934 Genomic DNA. Translation: DAA06915.1.
PIRiS48997.
RefSeqiNP_012088.3. NM_001179347.3.

Genome annotation databases

EnsemblFungiiYHR216W; YHR216W; YHR216W.
GeneIDi856626.
KEGGisce:YHR216W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00029 Genomic DNA. Translation: AAB69728.1.
BK006934 Genomic DNA. Translation: DAA06915.1.
PIRiS48997.
RefSeqiNP_012088.3. NM_001179347.3.

3D structure databases

ProteinModelPortaliP38697.
SMRiP38697.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36651. 62 interactors.
DIPiDIP-2840N.
IntActiP38697. 39 interactors.
MINTiMINT-521280.

Proteomic databases

MaxQBiP38697.
PRIDEiP38697.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYHR216W; YHR216W; YHR216W.
GeneIDi856626.
KEGGisce:YHR216W.

Organism-specific databases

EuPathDBiFungiDB:YHR216W.
SGDiS000001259. IMD2.

Phylogenomic databases

GeneTreeiENSGT00530000062923.
HOGENOMiHOG000165752.
KOiK00088.
OMAiRYFIESE.
OrthoDBiEOG092C1U8P.

Enzyme and pathway databases

UniPathwayiUPA00601; UER00295.
BioCyciYEAST:YHR216W-MONOMER.
ReactomeiR-SCE-6798695. Neutrophil degranulation.
R-SCE-73817. Purine ribonucleoside monophosphate biosynthesis.
R-SCE-74217. Purine salvage.
SABIO-RKP38697.

Miscellaneous databases

PROiP38697.

Family and domain databases

CDDicd00381. IMPDH. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01964. IMPDH. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR000644. CBS_dom.
IPR005990. IMP_DH.
IPR015875. IMP_DH/GMP_Rdtase_CS.
IPR001093. IMP_DH_GMPRt.
[Graphical view]
PANTHERiPTHR11911:SF6. PTHR11911:SF6. 2 hits.
PfamiPF00571. CBS. 2 hits.
PF00478. IMPDH. 1 hit.
[Graphical view]
PIRSFiPIRSF000130. IMPDH. 1 hit.
SMARTiSM00116. CBS. 2 hits.
[Graphical view]
TIGRFAMsiTIGR01302. IMP_dehydrog. 1 hit.
PROSITEiPS51371. CBS. 2 hits.
PS00487. IMP_DH_GMP_RED. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiIMDH2_YEAST
AccessioniPrimary (citable) accession number: P38697
Secondary accession number(s): D3DLH1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 158 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7870 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.