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P05373

- HEM2_YEAST

UniProt

P05373 - HEM2_YEAST

Protein

Delta-aminolevulinic acid dehydratase

Gene

HEM2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 151 (01 Oct 2014)
      Sequence version 2 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen.

    Catalytic activityi

    2 5-aminolevulinate = porphobilinogen + 2 H2O.

    Cofactori

    Binds 1 zinc ion per monomer.1 Publication

    Enzyme regulationi

    Inhibited by divalent lead ions.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi133 – 1331Zinc; catalytic
    Metal bindingi135 – 1351Zinc; catalytic
    Metal bindingi143 – 1431Zinc; catalytic
    Active sitei210 – 2101Schiff-base intermediate with substrate
    Binding sitei220 – 2201Substrate 1
    Binding sitei232 – 2321Substrate 1
    Active sitei263 – 2631Schiff-base intermediate with substrate
    Binding sitei290 – 2901Substrate 2
    Binding sitei329 – 3291Substrate 2

    GO - Molecular functioni

    1. lead ion binding Source: UniProtKB
    2. porphobilinogen synthase activity Source: UniProtKB
    3. zinc ion binding Source: UniProtKB

    GO - Biological processi

    1. heme biosynthetic process Source: UniProtKB
    2. protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Heme biosynthesis, Porphyrin biosynthesis

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:YGL040C-MONOMER.
    UniPathwayiUPA00251; UER00318.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Delta-aminolevulinic acid dehydratase (EC:4.2.1.24)
    Short name:
    ALADH
    Alternative name(s):
    Porphobilinogen synthase
    Gene namesi
    Name:HEM2
    Ordered Locus Names:YGL040C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGL040c.
    SGDiS000003008. HEM2.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 342342Delta-aminolevulinic acid dehydratasePRO_0000140534Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei254 – 2541Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP05373.
    PaxDbiP05373.
    PeptideAtlasiP05373.

    Expressioni

    Gene expression databases

    GenevestigatoriP05373.

    Interactioni

    Subunit structurei

    Homooctamer.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-8239,EBI-8239
    SRP1Q028211EBI-8239,EBI-1797
    TEM1P389871EBI-8239,EBI-19113

    Protein-protein interaction databases

    BioGridi33206. 63 interactions.
    DIPiDIP-4311N.
    IntActiP05373. 4 interactions.
    MINTiMINT-476599.
    STRINGi4932.YGL040C.

    Structurei

    Secondary structure

    1
    342
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi14 – 163
    Helixi19 – 213
    Beta strandi22 – 243
    Helixi25 – 306
    Beta strandi32 – 343
    Helixi38 – 403
    Beta strandi41 – 5010
    Beta strandi54 – 563
    Beta strandi58 – 603
    Beta strandi64 – 663
    Helixi68 – 8013
    Beta strandi85 – 917
    Helixi103 – 1064
    Helixi111 – 12212
    Beta strandi126 – 1327
    Turni135 – 1373
    Beta strandi138 – 1403
    Beta strandi142 – 1443
    Beta strandi150 – 1523
    Helixi154 – 17118
    Beta strandi174 – 1785
    Helixi185 – 19511
    Turni199 – 2013
    Beta strandi203 – 2119
    Beta strandi213 – 2153
    Helixi217 – 2237
    Beta strandi228 – 2303
    Turni233 – 2353
    Helixi242 – 25413
    Beta strandi258 – 2658
    Helixi266 – 2683
    Helixi269 – 27810
    Turni279 – 2813
    Beta strandi284 – 2885
    Helixi290 – 30112
    Helixi307 – 32014
    Beta strandi324 – 3285
    Helixi331 – 3377

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AW5X-ray2.30A1-340[»]
    1EB3X-ray1.75A1-340[»]
    1GJPX-ray1.80A1-340[»]
    1H7NX-ray1.60A1-342[»]
    1H7OX-ray1.75A1-341[»]
    1H7PX-ray1.64A1-342[»]
    1H7RX-ray2.00A1-342[»]
    1OHLX-ray1.60A1-342[»]
    1QMLX-ray3.00A1-342[»]
    1QNVX-ray2.50A1-342[»]
    1W31X-ray1.90A1-342[»]
    1YLVX-ray2.15A1-342[»]
    ProteinModelPortaliP05373.
    SMRiP05373. Positions 1-340.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP05373.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ALADH family.Curated

    Phylogenomic databases

    eggNOGiCOG0113.
    GeneTreeiENSGT00390000006998.
    HOGENOMiHOG000020323.
    KOiK01698.
    OMAiDHPTACY.
    OrthoDBiEOG779P7W.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR001731. Porphobilinogen_synth.
    [Graphical view]
    PANTHERiPTHR11458. PTHR11458. 1 hit.
    PfamiPF00490. ALAD. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001415. Porphbilin_synth. 1 hit.
    PRINTSiPR00144. DALDHYDRTASE.
    SMARTiSM01004. ALAD. 1 hit.
    [Graphical view]
    PROSITEiPS00169. D_ALA_DEHYDRATASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P05373-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHTAEFLETE PTEISSVLAG GYNHPLLRQW QSERQLTKNM LIFPLFISDN    50
    PDDFTEIDSL PNINRIGVNR LKDYLKPLVA KGLRSVILFG VPLIPGTKDP 100
    VGTAADDPAG PVIQGIKFIR EYFPELYIIC DVCLCEYTSH GHCGVLYDDG 150
    TINRERSVSR LAAVAVNYAK AGAHCVAPSD MIDGRIRDIK RGLINANLAH 200
    KTFVLSYAAK FSGNLYGPFR DAACSAPSNG DRKCYQLPPA GRGLARRALE 250
    RDMSEGADGI IVKPSTFYLD IMRDASEICK DLPICAYHVS GEYAMLHAAA 300
    EKGVVDLKTI AFESHQGFLR AGARLIITYL APEFLDWLDE EN 342
    Length:342
    Mass (Da):37,740
    Last modified:October 1, 1996 - v2
    Checksum:i72F6EB11008BDF52
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti291 – 2911G → D in AAA34669. (PubMed:2445751)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03493 Genomic DNA. Translation: AAA34669.1.
    Z72562 Genomic DNA. Translation: CAA96742.1.
    AY692744 Genomic DNA. Translation: AAT92763.1.
    BK006941 Genomic DNA. Translation: DAA08060.1.
    PIRiS64042.
    RefSeqiNP_011475.1. NM_001180905.1.

    Genome annotation databases

    EnsemblFungiiYGL040C; YGL040C; YGL040C.
    GeneIDi852842.
    KEGGisce:YGL040C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03493 Genomic DNA. Translation: AAA34669.1 .
    Z72562 Genomic DNA. Translation: CAA96742.1 .
    AY692744 Genomic DNA. Translation: AAT92763.1 .
    BK006941 Genomic DNA. Translation: DAA08060.1 .
    PIRi S64042.
    RefSeqi NP_011475.1. NM_001180905.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AW5 X-ray 2.30 A 1-340 [» ]
    1EB3 X-ray 1.75 A 1-340 [» ]
    1GJP X-ray 1.80 A 1-340 [» ]
    1H7N X-ray 1.60 A 1-342 [» ]
    1H7O X-ray 1.75 A 1-341 [» ]
    1H7P X-ray 1.64 A 1-342 [» ]
    1H7R X-ray 2.00 A 1-342 [» ]
    1OHL X-ray 1.60 A 1-342 [» ]
    1QML X-ray 3.00 A 1-342 [» ]
    1QNV X-ray 2.50 A 1-342 [» ]
    1W31 X-ray 1.90 A 1-342 [» ]
    1YLV X-ray 2.15 A 1-342 [» ]
    ProteinModelPortali P05373.
    SMRi P05373. Positions 1-340.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33206. 63 interactions.
    DIPi DIP-4311N.
    IntActi P05373. 4 interactions.
    MINTi MINT-476599.
    STRINGi 4932.YGL040C.

    Proteomic databases

    MaxQBi P05373.
    PaxDbi P05373.
    PeptideAtlasi P05373.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGL040C ; YGL040C ; YGL040C .
    GeneIDi 852842.
    KEGGi sce:YGL040C.

    Organism-specific databases

    CYGDi YGL040c.
    SGDi S000003008. HEM2.

    Phylogenomic databases

    eggNOGi COG0113.
    GeneTreei ENSGT00390000006998.
    HOGENOMi HOG000020323.
    KOi K01698.
    OMAi DHPTACY.
    OrthoDBi EOG779P7W.

    Enzyme and pathway databases

    UniPathwayi UPA00251 ; UER00318 .
    BioCyci YEAST:YGL040C-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P05373.
    NextBioi 972420.
    PROi P05373.

    Gene expression databases

    Genevestigatori P05373.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    InterProi IPR013785. Aldolase_TIM.
    IPR001731. Porphobilinogen_synth.
    [Graphical view ]
    PANTHERi PTHR11458. PTHR11458. 1 hit.
    Pfami PF00490. ALAD. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001415. Porphbilin_synth. 1 hit.
    PRINTSi PR00144. DALDHYDRTASE.
    SMARTi SM01004. ALAD. 1 hit.
    [Graphical view ]
    PROSITEi PS00169. D_ALA_DEHYDRATASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of the yeast HEM2 gene and transcriptional regulation of COX5 and COR1 by heme."
      Myers A.M., Crivellone M.D., Koerner T.J., Tzagoloff A.
      J. Biol. Chem. 262:16822-16829(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes."
      Feuermann M., de Montigny J., Potier S., Souciet J.-L.
      Yeast 13:861-869(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
      Strain: ATCC 204508 / S288c.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "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-254, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH LEAD IONS, SUBUNIT, ENZYME REGULATION, ACTIVE SITE.
    10. "The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid."
      Erskine P.T., Newbold R., Roper J., Coker A., Warren M.J., Shoolingin-Jordan P.M., Wood S.P., Cooper J.B.
      Protein Sci. 8:1250-1256(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH LAEVULINIC ACID AND ZINC IONS, COFACTOR, ACTIVE SITE.
    11. "MAD analyses of yeast 5-aminolaevulinate dehydratase: their use in structure determination and in defining the metal-binding sites."
      Erskine P.T., Duke E.M., Tickle I.J., Senior N.M., Warren M.J., Cooper J.B.
      Acta Crystallogr. D 56:421-430(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH MERCURY IONS.
    12. "The X-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with two diacid inhibitors."
      Erskine P.T., Coates L., Newbold R., Brindley A.A., Stauffer F., Wood S.P., Warren M.J., Cooper J.B., Shoolingin-Jordan P.M., Neier R.
      FEBS Lett. 503:196-200(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEXES WITH ZINC IONS; 4-OXOSEBACIC ACID AND 4,7-DIOXOSEBACIC ACID, ACTIVE SITE.
    13. "The X-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with substrate and three inhibitors."
      Erskine P.T., Newbold R., Brindley A.A., Wood S.P., Shoolingin-Jordan P.M., Warren M.J., Cooper J.B.
      J. Mol. Biol. 312:133-141(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEXES WITH ZINC IONS; 5-AMINOLAEVULINIC ACID AND SUBSTRATE ANALOGS, ACTIVE SITE, SUBUNIT.

    Entry informationi

    Entry nameiHEM2_YEAST
    AccessioniPrimary (citable) accession number: P05373
    Secondary accession number(s): D6VU99
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 151 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 11600 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3