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P06983

- HEM3_ECOLI

UniProt

P06983 - HEM3_ECOLI

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Protein

Porphobilinogen deaminase

Gene

hemC

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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

dipyrromethaneNote: 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
Complete GO annotation...

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
Complete GO annotation...

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 – 106Combined sources
Helixi14 – 3017Combined sources
Beta strandi35 – 406Combined sources
Helixi44 – 474Combined sources
Helixi63 – 719Combined sources
Beta strandi76 – 816Combined sources
Helixi82 – 843Combined sources
Beta strandi93 – 986Combined sources
Beta strandi106 – 1094Combined sources
Helixi116 – 1183Combined sources
Beta strandi124 – 1263Combined sources
Helixi130 – 13910Combined sources
Beta strandi143 – 1464Combined sources
Helixi152 – 1609Combined sources
Beta strandi165 – 1706Combined sources
Helixi171 – 1766Combined sources
Helixi180 – 1823Combined sources
Beta strandi184 – 1863Combined sources
Turni189 – 1913Combined sources
Turni196 – 1994Combined sources
Beta strandi201 – 2066Combined sources
Helixi210 – 2167Combined sources
Helixi217 – 2193Combined sources
Helixi222 – 23817Combined sources
Beta strandi242 – 2443Combined sources
Beta strandi246 – 2538Combined sources
Beta strandi256 – 2649Combined sources
Beta strandi271 – 2788Combined sources
Helixi280 – 2823Combined sources
Helixi283 – 29614Combined sources
Helixi299 – 3046Combined sources
Turni305 – 3084Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
SMRiP06983. Positions 3-307.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06983.

Family & Domainsi

Sequence similaritiesi

Belongs to the HMBS family.Curated

Phylogenomic databases

eggNOGiCOG0181.
HOGENOMiHOG000228588.
InParanoidiP06983.
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

        10         20         30         40         50
MLDNVLRIAT RQSPLALWQA HYVKDKLMAS HPGLVVELVP MVTRGDVILD
60 70 80 90 100
TPLAKVGGKG LFVKELEVAL LENRADIAVH SMKDVPVEFP QGLGLVTICE
110 120 130 140 150
REDPRDAFVS NNYDSLDALP AGSIVGTSSL RRQCQLAERR PDLIIRSLRG
160 170 180 190 200
NVGTRLSKLD NGEYDAIILA VAGLKRLGLE SRIRAALPPE ISLPAVGQGA
210 220 230 240 250
VGIECRLDDS RTRELLAALN HHETALRVTA ERAMNTRLEG GCQVPIGSYA
260 270 280 290 300
ELIDGEIWLR ALVGAPDGSQ IIRGERRGAP QDAEQMGISL AEELLNNGAR
310
EILAEVYNGD APA
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. Curated

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
SMRi P06983. Positions 3-307.
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.
InParanoidi P06983.
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

« Hide 'large scale' publications
  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: PROSTHETIC GROUP 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), PROSTHETIC GROUP 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: November 26, 2014
This is version 160 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