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P0ACB2

- HEM2_ECOLI

UniProt

P0ACB2 - HEM2_ECOLI

Protein

Delta-aminolevulinic acid dehydratase

Gene

hemB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 80 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      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.4 Publications

    Enzyme regulationi

    Allosteric enzyme. Stimulated by magnesium ions.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi120 – 1201Zinc; catalytic2 Publications
    Metal bindingi122 – 1221Zinc; catalytic2 Publications
    Metal bindingi130 – 1301Zinc; catalytic2 Publications
    Active sitei195 – 1951Schiff-base intermediate with substrate
    Binding sitei205 – 2051Substrate 1
    Binding sitei216 – 2161Substrate 1
    Metal bindingi232 – 2321Magnesium2 Publications
    Active sitei247 – 2471Schiff-base intermediate with substrate
    Binding sitei273 – 2731Substrate 2
    Binding sitei312 – 3121Substrate 2

    GO - Molecular functioni

    1. metal ion binding Source: EcoCyc
    2. porphobilinogen synthase activity Source: EcoCyc
    3. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. heme biosynthetic process Source: EcoliWiki
    2. protoporphyrinogen IX biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Heme biosynthesis, Porphyrin biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:PORPHOBILSYNTH-MONOMER.
    ECOL316407:JW0361-MONOMER.
    MetaCyc:PORPHOBILSYNTH-MONOMER.
    UniPathwayiUPA00251; UER00318.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Delta-aminolevulinic acid dehydratase (EC:4.2.1.24)
    Short name:
    ALAD
    Short name:
    ALADH
    Alternative name(s):
    Porphobilinogen synthase
    Gene namesi
    Name:hemB
    Synonyms:ncf
    Ordered Locus Names:b0369, JW0361
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10428. hemB.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: UniProtKB

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi127 – 1271H → A: No significant effect on activity; when associated with A-129. 1 Publication
    Mutagenesisi129 – 1291H → A: No significant effect on activity; when associated with A-127. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 324323Delta-aminolevulinic acid dehydratasePRO_0000140501Add
    BLAST

    Proteomic databases

    PaxDbiP0ACB2.
    PRIDEiP0ACB2.

    2D gel databases

    SWISS-2DPAGEP0ACB2.

    Expressioni

    Gene expression databases

    GenevestigatoriP0ACB2.

    Interactioni

    Subunit structurei

    Homooctamer.3 Publications

    Protein-protein interaction databases

    DIPiDIP-36209N.
    IntActiP0ACB2. 6 interactions.
    MINTiMINT-6765615.
    STRINGi511145.b0369.

    Structurei

    Secondary structure

    1
    324
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 125
    Helixi15 – 217
    Helixi28 – 303
    Beta strandi31 – 388
    Beta strandi48 – 503
    Beta strandi54 – 574
    Helixi58 – 603
    Helixi61 – 7010
    Beta strandi75 – 817
    Beta strandi86 – 883
    Helixi90 – 934
    Helixi98 – 10912
    Beta strandi113 – 1197
    Turni122 – 1243
    Beta strandi125 – 1273
    Beta strandi129 – 1335
    Beta strandi135 – 1384
    Helixi140 – 15718
    Beta strandi160 – 1645
    Helixi171 – 18111
    Beta strandi188 – 1903
    Beta strandi194 – 1963
    Helixi199 – 2013
    Helixi202 – 2087
    Turni217 – 2193
    Helixi226 – 23813
    Beta strandi242 – 2487
    Helixi250 – 2523
    Helixi253 – 2608
    Beta strandi267 – 2715
    Helixi273 – 28412
    Helixi290 – 30314
    Beta strandi307 – 3115
    Helixi314 – 3196

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B4EX-ray2.00A2-324[»]
    1I8JX-ray1.90A/B2-324[»]
    1L6SX-ray1.70A/B2-324[»]
    1L6YX-ray1.90A/B2-324[»]
    ProteinModelPortaliP0ACB2.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0ACB2.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ALADH family.Curated

    Phylogenomic databases

    eggNOGiCOG0113.
    HOGENOMiHOG000020323.
    KOiK01698.
    OMAiQMNPANR.
    OrthoDBiEOG6VXFCB.
    PhylomeDBiP0ACB2.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0ACB2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTDLIQRPRR LRKSPALRAM FEETTLSLND LVLPIFVEEE IDDYKAVEAM    50
    PGVMRIPEKH LAREIERIAN AGIRSVMTFG ISHHTDETGS DAWREDGLVA 100
    RMSRICKQTV PEMIVMSDTC FCEYTSHGHC GVLCEHGVDN DATLENLGKQ 150
    AVVAAAAGAD FIAPSAAMDG QVQAIRQALD AAGFKDTAIM SYSTKFASSF 200
    YGPFREAAGS ALKGDRKSYQ MNPMNRREAI RESLLDEAQG ADCLMVKPAG 250
    AYLDIVRELR ERTELPIGAY QVSGEYAMIK FAALAGAIDE EKVVLESLGS 300
    IKRAGADLIF SYFALDLAEK KILR 324
    Length:324
    Mass (Da):35,625
    Last modified:January 23, 2007 - v2
    Checksum:iCE814E5705BFD255
    GO

    Sequence cautioni

    The sequence AAB18092.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.
    The sequence BAA12842.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti18 – 192RA → PR in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti19 – 4224AMFEE…EEEID → VCLKRQHLSLTTWCCRSLLK KKLT in CAA35467. (PubMed:2464127)CuratedAdd
    BLAST
    Sequence conflicti90 – 912SD → ER in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti104 – 1041R → P in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti226 – 2261R → P in CAA35467. (PubMed:2464127)Curated
    Sequence conflicti227 – 2271R → A in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti229 – 2291A → G in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti231 – 2311R → A in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti233 – 2331S → Y in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti241 – 2411A → P in AAA62629. (PubMed:2656410)Curated
    Sequence conflicti254 – 2541D → N in AAA62629. (PubMed:2656410)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M24488 Genomic DNA. Translation: AAA62629.1.
    X17417 Genomic DNA. Translation: CAA35467.1.
    L44595 Genomic DNA. Translation: AAB52499.1.
    D85613 Genomic DNA. Translation: BAA12842.1. Different initiation.
    U73857 Genomic DNA. Translation: AAB18092.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73472.2.
    AP009048 Genomic DNA. Translation: BAE76150.1.
    PIRiA64765. SYECPF.
    RefSeqiNP_414903.4. NC_000913.3.
    YP_488662.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73472; AAC73472; b0369.
    BAE76150; BAE76150; BAE76150.
    GeneIDi12932508.
    945017.
    KEGGiecj:Y75_p0358.
    eco:b0369.
    PATRICi32115877. VBIEscCol129921_0380.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M24488 Genomic DNA. Translation: AAA62629.1 .
    X17417 Genomic DNA. Translation: CAA35467.1 .
    L44595 Genomic DNA. Translation: AAB52499.1 .
    D85613 Genomic DNA. Translation: BAA12842.1 . Different initiation.
    U73857 Genomic DNA. Translation: AAB18092.1 . Different initiation.
    U00096 Genomic DNA. Translation: AAC73472.2 .
    AP009048 Genomic DNA. Translation: BAE76150.1 .
    PIRi A64765. SYECPF.
    RefSeqi NP_414903.4. NC_000913.3.
    YP_488662.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B4E X-ray 2.00 A 2-324 [» ]
    1I8J X-ray 1.90 A/B 2-324 [» ]
    1L6S X-ray 1.70 A/B 2-324 [» ]
    1L6Y X-ray 1.90 A/B 2-324 [» ]
    ProteinModelPortali P0ACB2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36209N.
    IntActi P0ACB2. 6 interactions.
    MINTi MINT-6765615.
    STRINGi 511145.b0369.

    Chemistry

    BindingDBi P0ACB2.

    2D gel databases

    SWISS-2DPAGE P0ACB2.

    Proteomic databases

    PaxDbi P0ACB2.
    PRIDEi P0ACB2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73472 ; AAC73472 ; b0369 .
    BAE76150 ; BAE76150 ; BAE76150 .
    GeneIDi 12932508.
    945017.
    KEGGi ecj:Y75_p0358.
    eco:b0369.
    PATRICi 32115877. VBIEscCol129921_0380.

    Organism-specific databases

    EchoBASEi EB0423.
    EcoGenei EG10428. hemB.

    Phylogenomic databases

    eggNOGi COG0113.
    HOGENOMi HOG000020323.
    KOi K01698.
    OMAi QMNPANR.
    OrthoDBi EOG6VXFCB.
    PhylomeDBi P0ACB2.

    Enzyme and pathway databases

    UniPathwayi UPA00251 ; UER00318 .
    BioCyci EcoCyc:PORPHOBILSYNTH-MONOMER.
    ECOL316407:JW0361-MONOMER.
    MetaCyc:PORPHOBILSYNTH-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0ACB2.
    PROi P0ACB2.

    Gene expression databases

    Genevestigatori P0ACB2.

    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. "The structure of the Escherichia coli hemB gene."
      Li J.-M., Russell C.S., Cosloy S.D.
      Gene 75:177-184(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Nucleotide sequence of the hemB gene of Escherichia coli K12."
      Echelard Y., Dymetryszyn J., Drolet M., Sasarman A.
      Mol. Gen. Genet. 214:503-508(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. Sigurdsson E., Backman V.M., Eggertsson G.
      Submitted (AUG-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. Nashimoto H., Saito N.
      Submitted (NOV-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    5. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    7. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    8. "Purification and characterization of 5-aminolaevulinic acid dehydratase from Escherichia coli and a study of the reactive thiols at the metal-binding domain."
      Spencer P., Jordan P.M.
      Biochem. J. 290:279-287(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 2-6; 96-135 AND 238-254.
    9. "The phylogenetically conserved histidines of Escherichia coli porphobilinogen synthase are not required for catalysis."
      Mitchell L.W., Volin M., Jaffe E.K.
      J. Biol. Chem. 270:24054-24059(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, ENZYME REGULATION, MUTAGENESIS OF HIS-127 AND HIS-129.
    10. "X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0-A resolution."
      Erskine P.T., Norton E., Cooper J.B., Lambert R., Coker A., Lewis G., Spencer P., Sarwar M., Wood S.P., Warren M.J., Shoolingin-Jordan P.M.
      Biochemistry 38:4266-4276(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH LEVULINIC ACID AND ZINC IONS, SUBUNIT, COFACTOR.
    11. "Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity."
      Kervinen J., Jaffe E.K., Stauffer F., Neier R., Wlodawer A., Zdanov A.
      Biochemistry 40:8227-8236(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH 4,7-DIOXOSEBACIC ACID; ZINC AND MAGNESIUM, ACTIVE SITE, SUBUNIT, COFACTOR.
    12. "Species-specific inhibition of porphobilinogen synthase by 4-oxosebacic acid."
      Jaffe E.K., Kervinen J., Martins J., Stauffer F., Neier R., Wlodawer A., Zdanov A.
      J. Biol. Chem. 277:19792-19799(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH 4-OXOSEBACIC ACID; ZINC AND MAGNESIUM, ACTIVE SITE, SUBUNIT, COFACTOR.

    Entry informationi

    Entry nameiHEM2_ECOLI
    AccessioniPrimary (citable) accession number: P0ACB2
    Secondary accession number(s): P15002, P78247, Q2MC56
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 80 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3