Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Porphobilinogen deaminase

Gene

hemC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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: protoporphyrin-IX biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Delta-aminolevulinic acid dehydratase (hemB)
  2. Porphobilinogen deaminase (hemC)
  3. Uroporphyrinogen-III synthase (hemD)
  4. Uroporphyrinogen decarboxylase (hemE)
This subpathway is part of the pathway protoporphyrin-IX biosynthesis, which is itself part of Porphyrin-containing compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate, the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

GO - Molecular functioni

  • hydroxymethylbilane synthase activity Source: EcoCyc

GO - Biological processi

  • heme biosynthetic process Source: EcoliWiki
  • peptidyl-pyrromethane cofactor linkage Source: EcoliWiki
  • protoporphyrinogen IX biosynthetic process Source: EcoCyc
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10429. hemC.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi7R → L: No loss of activity. 1
Mutagenesisi11R → L: Loss of activity. 1
Mutagenesisi55K → Q: No loss of activity. 1 Publication1
Mutagenesisi59K → Q: 25-fold decrease in activity. 1 Publication1
Mutagenesisi101R → L: No loss of activity. 1
Mutagenesisi131R → L: Complete loss of activity. 1
Mutagenesisi132R → L: Complete loss of activity. 1
Mutagenesisi155R → L: Loss of activity. 1
Mutagenesisi176R → L: Loss of activity. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001429341 – 313Porphobilinogen deaminaseAdd BLAST313

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei242S-(dipyrrolylmethanemethyl)cysteine1

Proteomic databases

EPDiP06983.
PaxDbiP06983.
PRIDEiP06983.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

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

Structurei

Secondary structure

1313
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Helixi14 – 30Combined sources17
Beta strandi35 – 40Combined sources6
Helixi44 – 47Combined sources4
Helixi63 – 71Combined sources9
Beta strandi76 – 81Combined sources6
Helixi82 – 84Combined sources3
Beta strandi93 – 98Combined sources6
Beta strandi106 – 109Combined sources4
Helixi116 – 118Combined sources3
Beta strandi124 – 126Combined sources3
Helixi130 – 139Combined sources10
Beta strandi143 – 146Combined sources4
Helixi152 – 160Combined sources9
Beta strandi165 – 170Combined sources6
Helixi171 – 176Combined sources6
Helixi180 – 182Combined sources3
Beta strandi184 – 186Combined sources3
Turni189 – 191Combined sources3
Turni196 – 199Combined sources4
Beta strandi201 – 206Combined sources6
Helixi210 – 216Combined sources7
Helixi217 – 219Combined sources3
Helixi222 – 238Combined sources17
Beta strandi242 – 244Combined sources3
Beta strandi246 – 253Combined sources8
Beta strandi256 – 264Combined sources9
Beta strandi271 – 278Combined sources8
Helixi280 – 282Combined sources3
Helixi283 – 296Combined sources14
Helixi299 – 304Combined sources6
Turni305 – 308Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06983.

Family & Domainsi

Sequence similaritiesi

Belongs to the HMBS family.Curated

Phylogenomic databases

eggNOGiENOG4105D6W. Bacteria.
COG0181. LUCA.
HOGENOMiHOG000228588.
InParanoidiP06983.
KOiK01749.
OMAiGIECRTD.
PhylomeDBiP06983.

Family and domain databases

Gene3Di3.30.160.40. 1 hit.
HAMAPiMF_00260. Porphobil_deam. 1 hit.
InterProiIPR000860. HemC.
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 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti137A → G in AAA67601 (PubMed:1379743).Curated1
Sequence conflicti186A → G in AAA67601 (PubMed:1379743).Curated1
Sequence conflicti241G → A in CAA27813 (PubMed:3529035).Curated1
Sequence conflicti261A → G in CAA27813 (PubMed:3529035).Curated1
Sequence conflicti265A → R in AAA67601 (PubMed:1379743).Curated1

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.
RefSeqiWP_001338644.1. NZ_LN832404.1.
YP_026260.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAT48218; AAT48218; b3805.
BAE77496; BAE77496; BAE77496.
GeneIDi947759.
KEGGiecj:JW5932.
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.
PIRiF65184. IBEC.
RefSeqiWP_001338644.1. NZ_LN832404.1.
YP_026260.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

EPDiP06983.
PaxDbiP06983.
PRIDEiP06983.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAT48218; AAT48218; b3805.
BAE77496; BAE77496; BAE77496.
GeneIDi947759.
KEGGiecj:JW5932.
eco:b3805.
PATRICi32123109. VBIEscCol129921_3920.

Organism-specific databases

EchoBASEiEB0424.
EcoGeneiEG10429. hemC.

Phylogenomic databases

eggNOGiENOG4105D6W. Bacteria.
COG0181. LUCA.
HOGENOMiHOG000228588.
InParanoidiP06983.
KOiK01749.
OMAiGIECRTD.
PhylomeDBiP06983.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP06983.
PROiP06983.

Family and domain databases

Gene3Di3.30.160.40. 1 hit.
HAMAPiMF_00260. Porphobil_deam. 1 hit.
InterProiIPR000860. HemC.
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]
ProtoNetiSearch...

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 2, 2016
This is version 172 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.