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Protein

Inosine-5'-monophosphate dehydrogenase 4

Gene

IMD4

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.UniRule annotation2 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

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi331 – 3311Potassium; via carbonyl oxygenUniRule annotation
Metal bindingi333 – 3331Potassium; via carbonyl oxygenUniRule annotation
Binding sitei334 – 3341IMPUniRule annotation
Active sitei336 – 3361Thioimidate intermediateUniRule annotation
Metal bindingi336 – 3361Potassium; via carbonyl oxygenUniRule annotation
Binding sitei450 – 4501IMPUniRule annotation
Metal bindingi509 – 5091Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation
Metal bindingi510 – 5101Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation
Metal bindingi511 – 5111Potassium; via carbonyl oxygen; shared with tetrameric partnerUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi279 – 2813NADUniRule annotation
Nucleotide bindingi329 – 3313NADUniRule annotation

GO - Molecular functioni

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

GO - Biological processi

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:YML056C-MONOMER.
ReactomeiREACT_301060. Purine ribonucleoside monophosphate biosynthesis.
UniPathwayiUPA00601; UER00295.

Names & Taxonomyi

Protein namesi
Recommended name:
Inosine-5'-monophosphate dehydrogenase 4UniRule annotation (EC:1.1.1.205UniRule annotation)
Short name:
IMP dehydrogenase 4UniRule annotation
Short name:
IMPD 4UniRule annotation
Short name:
IMPDH 4UniRule annotation
Gene namesi
Name:IMD4UniRule annotation
Ordered Locus Names:YML056C
ORF Names:YM9958.06C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIII

Organism-specific databases

CYGDiYML056c.
EuPathDBiFungiDB:YML056C.
SGDiS000004520. IMD4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 524524Inosine-5'-monophosphate dehydrogenase 4PRO_0000093684Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei125 – 1251Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP50094.
PaxDbiP50094.
PeptideAtlasiP50094.

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

Binary interactionsi

WithEntry#Exp.IntActNotes
IMD3P500956EBI-9195,EBI-9190

Protein-protein interaction databases

BioGridi35111. 86 interactions.
DIPiDIP-6458N.
IntActiP50094. 60 interactions.
MINTiMINT-675699.
STRINGi4932.YML056C.

Structurei

3D structure databases

ProteinModelPortaliP50094.
SMRiP50094. Positions 6-523.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini122 – 18362CBS 1UniRule annotationAdd
BLAST
Domaini185 – 24157CBS 2UniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni369 – 3713IMP bindingUniRule annotation
Regioni392 – 3932IMP bindingUniRule annotation
Regioni416 – 4205IMP bindingUniRule annotation

Sequence similaritiesi

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

Keywords - Domaini

CBS domain, Repeat

Phylogenomic databases

eggNOGiCOG0517.
GeneTreeiENSGT00530000062923.
HOGENOMiHOG000165752.
KOiK00088.
OMAiTESSMAR.
OrthoDBiEOG793BHK.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01964. IMPDH.
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. 1 hit.
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.

P50094-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAAPLDYKK ALEHLKTYSS KDGLSVQELM DSTTRGGLTY NDFLVLPGLV
60 70 80 90 100
NFPSSAVSLQ TKLTKKITLN TPFVSSPMDT VTEADMAIYM ALLGGIGFIH
110 120 130 140 150
HNCTPKEQAS MVKKVKMFEN GFINSPIVIS PTTTVGEVKV MKRKFGFSGF
160 170 180 190 200
PVTEDGKCPG KLVGLVTSRD IQFLEDDSLV VSEVMTKNPV TGIKGITLKE
210 220 230 240 250
GNEILKQTKK GKLLIVDDNG NLVSMLSRAD LMKNQNYPLA SKSATTKQLL
260 270 280 290 300
CGAAIGTIEA DKERLRLLVE AGLDVVILDS SQGNSVFQLN MIKWIKETFP
310 320 330 340 350
DLEIIAGNVA TREQAANLIA AGADGLRIGM GSGSICITQE VMACGRPQGT
360 370 380 390 400
AVYNVCQFAN QFGVPCMADG GVQNIGHITK ALALGSSTVM MGGMLAGTTE
410 420 430 440 450
SPGEYFYKDG KRLKAYRGMG SIDAMQKTGN KGNASTSRYF SESDSVLVAQ
460 470 480 490 500
GVSGAVVDKG SIKKFIPYLY NGLQHSCQDI GCESLTSLKE NVQNGEVRFE
510 520
FRTASAQLEG GVHNLHSYEK RLYN
Length:524
Mass (Da):56,394
Last modified:October 1, 1996 - v1
Checksum:iA73D1E4EFE8AEAD9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46729 Genomic DNA. Translation: CAA86719.1.
AY899250 mRNA. Translation: AAX83935.1.
BK006946 Genomic DNA. Translation: DAA09842.1.
PIRiS50890.
RefSeqiNP_013656.1. NM_001182414.1.

Genome annotation databases

EnsemblFungiiYML056C; YML056C; YML056C.
GeneIDi854948.
KEGGisce:YML056C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46729 Genomic DNA. Translation: CAA86719.1.
AY899250 mRNA. Translation: AAX83935.1.
BK006946 Genomic DNA. Translation: DAA09842.1.
PIRiS50890.
RefSeqiNP_013656.1. NM_001182414.1.

3D structure databases

ProteinModelPortaliP50094.
SMRiP50094. Positions 6-523.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35111. 86 interactions.
DIPiDIP-6458N.
IntActiP50094. 60 interactions.
MINTiMINT-675699.
STRINGi4932.YML056C.

Proteomic databases

MaxQBiP50094.
PaxDbiP50094.
PeptideAtlasiP50094.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYML056C; YML056C; YML056C.
GeneIDi854948.
KEGGisce:YML056C.

Organism-specific databases

CYGDiYML056c.
EuPathDBiFungiDB:YML056C.
SGDiS000004520. IMD4.

Phylogenomic databases

eggNOGiCOG0517.
GeneTreeiENSGT00530000062923.
HOGENOMiHOG000165752.
KOiK00088.
OMAiTESSMAR.
OrthoDBiEOG793BHK.

Enzyme and pathway databases

UniPathwayiUPA00601; UER00295.
BioCyciYEAST:YML056C-MONOMER.
ReactomeiREACT_301060. Purine ribonucleoside monophosphate biosynthesis.

Miscellaneous databases

NextBioi978010.
PROiP50094.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01964. IMPDH.
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. 1 hit.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE."
    Zhang Z., Dietrich F.S.
    Nucleic Acids Res. 33:2838-2851(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-83.
    Strain: ATCC 208353 / W303-1A.
  4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast."
    Hyle J.W., Shaw R.J., Reines D.
    J. Biol. Chem. 278:28470-28478(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Detection of the mycophenolate-inhibited form of IMP dehydrogenase in vivo."
    McPhillips C.C., Hyle J.W., Reines D.
    Proc. Natl. Acad. Sci. U.S.A. 101:12171-12176(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-125, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiIMDH4_YEAST
AccessioniPrimary (citable) accession number: P50094
Secondary accession number(s): D6VZB8, Q2VQW8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 24, 2015
This is version 143 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 2970 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 XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3

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 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.