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P05373

- HEM2_YEAST

UniProt

P05373 - HEM2_YEAST

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Protein
Delta-aminolevulinic acid dehydratase
Gene
HEM2, YGL040C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 substrate4 Publications
Binding sitei220 – 2201Substrate 1
Binding sitei232 – 2321Substrate 1
Active sitei263 – 2631Schiff-base intermediate with substrate4 Publications
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
Complete GO annotation...

GO - Biological processi

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

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 dehydratase
PRO_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.2 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

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.

Miscellaneous databases

EvolutionaryTraceiP05373.

Family & Domainsi

Sequence similaritiesi

Belongs to the ALADH family.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti291 – 2911G → D in AAA34669. 1 Publication

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...

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 150 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.

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

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