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P06983

- HEM3_ECOLI

UniProt

P06983 - HEM3_ECOLI

Protein

Porphobilinogen deaminase

Gene

hemC

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 158 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.1 Publication

    Catalytic activityi

    4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3.

    Cofactori

    Binds 1 dipyrromethane group covalently.

    Pathwayi

    GO - Molecular functioni

    1. hydroxymethylbilane synthase activity Source: EcoCyc

    GO - Biological processi

    1. heme biosynthetic process Source: EcoliWiki
    2. peptidyl-pyrromethane cofactor linkage Source: EcoliWiki
    3. protoporphyrinogen IX biosynthetic process Source: EcoCyc
    4. tetrapyrrole biosynthetic process Source: EcoliWiki

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Porphyrin biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:OHMETHYLBILANESYN-MONOMER.
    ECOL316407:JW5932-MONOMER.
    MetaCyc:OHMETHYLBILANESYN-MONOMER.
    UniPathwayiUPA00251; UER00319.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Porphobilinogen deaminase (EC:2.5.1.61)
    Short name:
    PBG
    Alternative name(s):
    Hydroxymethylbilane synthase
    Short name:
    HMBS
    Pre-uroporphyrinogen synthase
    Gene namesi
    Name:hemC
    Synonyms:popE
    Ordered Locus Names:b3805, JW5932
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10429. hemC.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi7 – 71R → L: No loss of activity.
    Mutagenesisi11 – 111R → L: Loss of activity.
    Mutagenesisi55 – 551K → Q: No loss of activity. 1 Publication
    Mutagenesisi59 – 591K → Q: 25-fold decrease in activity. 1 Publication
    Mutagenesisi101 – 1011R → L: No loss of activity.
    Mutagenesisi131 – 1311R → L: Complete loss of activity.
    Mutagenesisi132 – 1321R → L: Complete loss of activity.
    Mutagenesisi155 – 1551R → L: Loss of activity.
    Mutagenesisi176 – 1761R → L: Loss of activity.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 313313Porphobilinogen deaminasePRO_0000142934Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei242 – 2421S-(dipyrrolylmethanemethyl)cysteine

    Proteomic databases

    PaxDbiP06983.
    PRIDEiP06983.

    Expressioni

    Gene expression databases

    GenevestigatoriP06983.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-9879N.
    IntActiP06983. 1 interaction.
    MINTiMINT-1302039.
    STRINGi511145.b3805.

    Structurei

    Secondary structure

    1
    313
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106
    Helixi14 – 3017
    Beta strandi35 – 406
    Helixi44 – 474
    Helixi63 – 719
    Beta strandi76 – 816
    Helixi82 – 843
    Beta strandi93 – 986
    Beta strandi106 – 1094
    Helixi116 – 1183
    Beta strandi124 – 1263
    Helixi130 – 13910
    Beta strandi143 – 1464
    Helixi152 – 1609
    Beta strandi165 – 1706
    Helixi171 – 1766
    Helixi180 – 1823
    Beta strandi184 – 1863
    Turni189 – 1913
    Turni196 – 1994
    Beta strandi201 – 2066
    Helixi210 – 2167
    Helixi217 – 2193
    Helixi222 – 23817
    Beta strandi242 – 2443
    Beta strandi246 – 2538
    Beta strandi256 – 2649
    Beta strandi271 – 2788
    Helixi280 – 2823
    Helixi283 – 29614
    Helixi299 – 3046
    Turni305 – 3084

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AH5X-ray2.40A1-313[»]
    1GTKX-ray1.66A1-313[»]
    1PDAX-ray1.76A1-313[»]
    1YPNX-ray2.30A1-313[»]
    2YPNX-ray2.30A1-313[»]
    ProteinModelPortaliP06983.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP06983.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the HMBS family.Curated

    Phylogenomic databases

    eggNOGiCOG0181.
    HOGENOMiHOG000228588.
    KOiK01749.
    OMAiGIECRTD.
    OrthoDBiEOG6HB9Z6.
    PhylomeDBiP06983.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam.
    InterProiIPR000860. 4pyrrol_synth_OHMeBilane_synth.
    IPR022419. Porphobilin_deaminase_cofac_BS.
    IPR022417. Porphobilin_deaminase_N.
    IPR022418. Porphobilinogen_deaminase_C.
    [Graphical view]
    PANTHERiPTHR11557. PTHR11557. 1 hit.
    PfamiPF01379. Porphobil_deam. 1 hit.
    PF03900. Porphobil_deamC. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
    PRINTSiPR00151. PORPHBDMNASE.
    SUPFAMiSSF54782. SSF54782. 1 hit.
    TIGRFAMsiTIGR00212. hemC. 1 hit.
    PROSITEiPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P06983-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLDNVLRIAT RQSPLALWQA HYVKDKLMAS HPGLVVELVP MVTRGDVILD    50
    TPLAKVGGKG LFVKELEVAL LENRADIAVH SMKDVPVEFP QGLGLVTICE 100
    REDPRDAFVS NNYDSLDALP AGSIVGTSSL RRQCQLAERR PDLIIRSLRG 150
    NVGTRLSKLD NGEYDAIILA VAGLKRLGLE SRIRAALPPE ISLPAVGQGA 200
    VGIECRLDDS RTRELLAALN HHETALRVTA ERAMNTRLEG GCQVPIGSYA 250
    ELIDGEIWLR ALVGAPDGSQ IIRGERRGAP QDAEQMGISL AEELLNNGAR 300
    EILAEVYNGD APA 313
    Length:313
    Mass (Da):33,852
    Last modified:November 1, 1997 - v2
    Checksum:i7276981B52C7D1E3
    GO

    Sequence cautioni

    The sequence AAA67601.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti137 – 1371A → G in AAA67601. (PubMed:1379743)Curated
    Sequence conflicti186 – 1861A → G in AAA67601. (PubMed:1379743)Curated
    Sequence conflicti241 – 2411G → A in CAA27813. (PubMed:3529035)Curated
    Sequence conflicti261 – 2611A → G in CAA27813. (PubMed:3529035)Curated
    Sequence conflicti265 – 2651A → R in AAA67601. (PubMed:1379743)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04242 Genomic DNA. Translation: CAA27813.1.
    X12614 Genomic DNA. Translation: CAA31132.1.
    M87049 Genomic DNA. Translation: AAA67601.1. Different initiation.
    U00096 Genomic DNA. Translation: AAT48218.1.
    AP009048 Genomic DNA. Translation: BAE77496.1.
    X66782 Genomic DNA. Translation: CAA47279.1.
    PIRiF65184. IBEC.
    RefSeqiYP_026260.1. NC_000913.3.
    YP_491637.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAT48218; AAT48218; b3805.
    BAE77496; BAE77496; BAE77496.
    GeneIDi12930663.
    947759.
    KEGGiecj:Y75_p3373.
    eco:b3805.
    PATRICi32123109. VBIEscCol129921_3920.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04242 Genomic DNA. Translation: CAA27813.1 .
    X12614 Genomic DNA. Translation: CAA31132.1 .
    M87049 Genomic DNA. Translation: AAA67601.1 . Different initiation.
    U00096 Genomic DNA. Translation: AAT48218.1 .
    AP009048 Genomic DNA. Translation: BAE77496.1 .
    X66782 Genomic DNA. Translation: CAA47279.1 .
    PIRi F65184. IBEC.
    RefSeqi YP_026260.1. NC_000913.3.
    YP_491637.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AH5 X-ray 2.40 A 1-313 [» ]
    1GTK X-ray 1.66 A 1-313 [» ]
    1PDA X-ray 1.76 A 1-313 [» ]
    1YPN X-ray 2.30 A 1-313 [» ]
    2YPN X-ray 2.30 A 1-313 [» ]
    ProteinModelPortali P06983.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9879N.
    IntActi P06983. 1 interaction.
    MINTi MINT-1302039.
    STRINGi 511145.b3805.

    Proteomic databases

    PaxDbi P06983.
    PRIDEi P06983.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAT48218 ; AAT48218 ; b3805 .
    BAE77496 ; BAE77496 ; BAE77496 .
    GeneIDi 12930663.
    947759.
    KEGGi ecj:Y75_p3373.
    eco:b3805.
    PATRICi 32123109. VBIEscCol129921_3920.

    Organism-specific databases

    EchoBASEi EB0424.
    EcoGenei EG10429. hemC.

    Phylogenomic databases

    eggNOGi COG0181.
    HOGENOMi HOG000228588.
    KOi K01749.
    OMAi GIECRTD.
    OrthoDBi EOG6HB9Z6.
    PhylomeDBi P06983.

    Enzyme and pathway databases

    UniPathwayi UPA00251 ; UER00319 .
    BioCyci EcoCyc:OHMETHYLBILANESYN-MONOMER.
    ECOL316407:JW5932-MONOMER.
    MetaCyc:OHMETHYLBILANESYN-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P06983.
    PROi P06983.

    Gene expression databases

    Genevestigatori P06983.

    Family and domain databases

    Gene3Di 3.30.160.40. 1 hit.
    HAMAPi MF_00260. Porphobil_deam.
    InterProi IPR000860. 4pyrrol_synth_OHMeBilane_synth.
    IPR022419. Porphobilin_deaminase_cofac_BS.
    IPR022417. Porphobilin_deaminase_N.
    IPR022418. Porphobilinogen_deaminase_C.
    [Graphical view ]
    PANTHERi PTHR11557. PTHR11557. 1 hit.
    Pfami PF01379. Porphobil_deam. 1 hit.
    PF03900. Porphobil_deamC. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
    PRINTSi PR00151. PORPHBDMNASE.
    SUPFAMi SSF54782. SSF54782. 1 hit.
    TIGRFAMsi TIGR00212. hemC. 1 hit.
    PROSITEi PS00533. PORPHOBILINOGEN_DEAM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the hemC locus encoding porphobilinogen deaminase of Escherichia coli K12."
      Thomas S.D., Jordan P.M.
      Nucleic Acids Res. 14:6215-6226(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-6, FUNCTION, SUBUNIT.
      Strain: K12.
    2. "The sequence of hemC, hemD and two additional E. coli genes."
      Alefounder P.R., Abell C., Battersby A.R.
      Nucleic Acids Res. 16:9871-9871(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / CS520.
    3. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
      Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
      Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 137.
      Strain: K12 / MG1655 / ATCC 47076.
    5. Cited for: SEQUENCE REVISION TO 186 AND 265.
    6. "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.
    7. "Comparative analysis of the cya locus in enterobacteria and related Gram-negative facultative anaerobes."
      Trotot P., Sismeiro O., Vivares C., Glaser P., Bresson-Roy A., Danchin A.
      Biochimie 78:277-287(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-89.
      Strain: K12.
    8. "Purification, crystallization and properties of porphobilinogen deaminase from a recombinant strain of Escherichia coli K12."
      Jordan P.M., Thomas S.D., Warren M.J.
      Biochem. J. 254:427-435(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-10.
    9. "Evidence that the pyrromethane cofactor of hydroxymethylbilane synthase (porphobilinogen deaminase) is bound to the protein through the sulphur atom of cysteine-242."
      Miller A.D., Hart G.J., Packman L.C., Battersby A.R.
      Biochem. J. 254:915-918(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: S-(DIPYRROLYLMETHANEMETHYL)CYSTEINE AT CYS-242.
    10. "Evidence that pyridoxal phosphate modification of lysine residues (Lys-55 and Lys-59) causes inactivation of hydroxymethylbilane synthase (porphobilinogen deaminase)."
      Miller A.D., Packman L.C., Hart G.J., Alefounder P.R., Abell C., Battersby A.R.
      Biochem. J. 262:119-124(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: INACTIVATION BY PYRIDOXAL 5'-PHOSPHATE.
    11. "Investigation of putative active-site lysine residues in hydroxymethylbilane synthase. Preparation and characterization of mutants in which (a) Lys-55, (b) Lys-59 and (c) both Lys-55 and Lys-59 have been replaced by glutamine."
      Hadener A., Alefounder P.R., Hart G.J., Abell C., Battersby A.R.
      Biochem. J. 271:487-491(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-55 AND LYS-59.
    12. "Studies on the mechanism of hydroxymethylbilane synthase concerning the role of arginine residues in substrate binding."
      Lander M., Pitt A.R., Alefounder P.R., Bardy D., Abell C., Battersby A.R.
      Biochem. J. 275:447-452(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ARGININE RESIDUES.
    13. "Mutagenesis of arginine residues in the catalytic cleft of Escherichia coli porphobilinogen deaminase that affects dipyrromethane cofactor assembly and tetrapyrrole chain initiation and elongation."
      Jordan P.M., Woodcock S.C.
      Biochem. J. 280:445-449(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ARGININE RESIDUES.
    14. "Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site."
      Louie G.V., Brownlie P.D., Labert R., Cooper J.B., Blundell T.L., Wood S.P., Warren M.J., Woodcock S.C., Jordan P.M.
      Nature 359:33-39(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), S-(DIPYRROLYLMETHANEMETHYL)CYSTEINE AT CYS-242.

    Entry informationi

    Entry nameiHEM3_ECOLI
    AccessioniPrimary (citable) accession number: P06983
    Secondary accession number(s): P78125, Q2M8B0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1988
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 158 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Arginine residues that are closely associated with one another might be involved in substrate binding.
    The porphobilinogen subunits are added to the dipyrromethane group.

    Keywords - Technical termi

    3D-structure, 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