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P06983 (HEM3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 153. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Porphobilinogen deaminase

Short name=PBG
EC=2.5.1.61
Alternative name(s):
Hydroxymethylbilane synthase
Short name=HMBS
Pre-uroporphyrinogen synthase
Gene names
Name:hemC
Synonyms:popE
Ordered Locus Names:b3805, JW5932
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length313 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. HAMAP-Rule MF_00260

Catalytic activity

4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3. HAMAP-Rule MF_00260

Cofactor

Binds 1 dipyrromethane group covalently.

Pathway

Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. HAMAP-Rule MF_00260

Subunit structure

Monomer.

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.

Sequence similarities

Belongs to the HMBS family.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 313313Porphobilinogen deaminase HAMAP-Rule MF_00260
PRO_0000142934

Amino acid modifications

Modified residue2421S-(dipyrrolylmethanemethyl)cysteine HAMAP-Rule MF_00260

Experimental info

Mutagenesis71R → L: No loss of activity. Ref.12 Ref.13
Mutagenesis111R → L: Loss of activity. Ref.12 Ref.13
Mutagenesis551K → Q: No loss of activity. Ref.11 Ref.12 Ref.13
Mutagenesis591K → Q: 25-fold decrease in activity. Ref.11 Ref.12 Ref.13
Mutagenesis1011R → L: No loss of activity. Ref.12 Ref.13
Mutagenesis1311R → L: Complete loss of activity. Ref.12 Ref.13
Mutagenesis1321R → L: Complete loss of activity. Ref.12 Ref.13
Mutagenesis1551R → L: Loss of activity. Ref.12 Ref.13
Mutagenesis1761R → L: Loss of activity. Ref.12 Ref.13
Sequence conflict1371A → G in AAA67601. Ref.3
Sequence conflict1861A → G in AAA67601. Ref.3
Sequence conflict2411G → A in CAA27813. Ref.1
Sequence conflict2611A → G in CAA27813. Ref.1
Sequence conflict2651A → R in AAA67601. Ref.3

Secondary structure

............................................................ 313
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06983 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 7276981B52C7D1E3

FASTA31333,852
        10         20         30         40         50         60 
MLDNVLRIAT RQSPLALWQA HYVKDKLMAS HPGLVVELVP MVTRGDVILD TPLAKVGGKG 

        70         80         90        100        110        120 
LFVKELEVAL LENRADIAVH SMKDVPVEFP QGLGLVTICE REDPRDAFVS NNYDSLDALP 

       130        140        150        160        170        180 
AGSIVGTSSL RRQCQLAERR PDLIIRSLRG NVGTRLSKLD NGEYDAIILA VAGLKRLGLE 

       190        200        210        220        230        240 
SRIRAALPPE ISLPAVGQGA VGIECRLDDS RTRELLAALN HHETALRVTA ERAMNTRLEG 

       250        260        270        280        290        300 
GCQVPIGSYA ELIDGEIWLR ALVGAPDGSQ IIRGERRGAP QDAEQMGISL AEELLNNGAR 

       310 
EILAEVYNGD APA 

« Hide

References

« Hide 'large scale' references
[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].
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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 137.
Strain: K12 / MG1655 / ATCC 47076.
[5]"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005."
Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L.
Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRIBEC. F65184.
RefSeqYP_026260.1. NC_000913.3.
YP_491637.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AH5X-ray2.40A1-313[»]
1GTKX-ray1.66A1-313[»]
1PDAX-ray1.76A1-313[»]
1YPNX-ray2.30A1-313[»]
2YPNX-ray2.30A1-313[»]
ProteinModelPortalP06983.
SMRP06983. Positions 3-307.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9879N.
IntActP06983. 1 interaction.
MINTMINT-1302039.
STRING511145.b3805.

Proteomic databases

PaxDbP06983.
PRIDEP06983.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAT48218; AAT48218; b3805.
BAE77496; BAE77496; BAE77496.
GeneID12930663.
947759.
KEGGecj:Y75_p3373.
eco:b3805.
PATRIC32123109. VBIEscCol129921_3920.

Organism-specific databases

EchoBASEEB0424.
EcoGeneEG10429. hemC.

Phylogenomic databases

eggNOGCOG0181.
HOGENOMHOG000228588.
KOK01749.
OMACITERED.
OrthoDBEOG6HB9Z6.
PhylomeDBP06983.
ProtClustDBPRK00072.

Enzyme and pathway databases

BioCycEcoCyc:OHMETHYLBILANESYN-MONOMER.
ECOL316407:JW5932-MONOMER.
MetaCyc:OHMETHYLBILANESYN-MONOMER.
UniPathwayUPA00251; UER00319.

Gene expression databases

GenevestigatorP06983.

Family and domain databases

Gene3D3.30.160.40. 1 hit.
HAMAPMF_00260. Porphobil_deam.
InterProIPR000860. 4pyrrol_synth_OHMeBilane_synth.
IPR022419. Porphobilin_deaminase_cofac_BS.
IPR022417. Porphobilin_deaminase_N.
IPR022418. Porphobilinogen_deaminase_C.
[Graphical view]
PANTHERPTHR11557. PTHR11557. 1 hit.
PfamPF01379. Porphobil_deam. 1 hit.
PF03900. Porphobil_deamC. 1 hit.
[Graphical view]
PIRSFPIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
PRINTSPR00151. PORPHBDMNASE.
SUPFAMSSF54782. SSF54782. 1 hit.
TIGRFAMsTIGR00212. hemC. 1 hit.
PROSITEPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP06983.
PROP06983.

Entry information

Entry nameHEM3_ECOLI
AccessionPrimary (citable) accession number: P06983
Secondary accession number(s): P78125, Q2M8B0
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 153 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene