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Protein

Uroporphyrinogen decarboxylase

Gene

hemE

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.1 Publication

Catalytic activityi

Uroporphyrinogen III = coproporphyrinogen + 4 CO2.

Pathwayi: protoporphyrin-IX biosynthesis

This protein is involved in step 4 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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei48 – 481SubstrateBy similarity
Binding sitei78 – 781SubstrateBy similarity
Sitei78 – 781Transition state stabilizerBy similarity
Binding sitei154 – 1541SubstrateBy similarity
Binding sitei209 – 2091SubstrateBy similarity
Binding sitei322 – 3221SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Porphyrin biosynthesis

Enzyme and pathway databases

BioCyciBSUB:BSU10120-MONOMER.
UniPathwayiUPA00251; UER00321.

Names & Taxonomyi

Protein namesi
Recommended name:
Uroporphyrinogen decarboxylase (EC:4.1.1.37)
Short name:
UPD
Short name:
URO-D
Gene namesi
Name:hemE
Ordered Locus Names:BSU10120
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 353353Uroporphyrinogen decarboxylasePRO_0000187584Add
BLAST

Proteomic databases

PaxDbiP32395.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005626.

Structurei

Secondary structure

1
353
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 156Combined sources
Beta strandi30 – 323Combined sources
Helixi36 – 5217Combined sources
Helixi54 – 6815Combined sources
Turni79 – 824Combined sources
Helixi83 – 864Combined sources
Beta strandi94 – 963Combined sources
Beta strandi99 – 1024Combined sources
Helixi107 – 1115Combined sources
Helixi118 – 1214Combined sources
Helixi123 – 13513Combined sources
Beta strandi141 – 1466Combined sources
Helixi148 – 15710Combined sources
Helixi165 – 1739Combined sources
Helixi175 – 19824Combined sources
Beta strandi202 – 2076Combined sources
Helixi211 – 2133Combined sources
Helixi216 – 2227Combined sources
Helixi224 – 23411Combined sources
Helixi235 – 2373Combined sources
Beta strandi241 – 2444Combined sources
Helixi249 – 2513Combined sources
Helixi252 – 2565Combined sources
Beta strandi261 – 2644Combined sources
Helixi271 – 2766Combined sources
Beta strandi281 – 2844Combined sources
Helixi289 – 2935Combined sources
Helixi296 – 31015Combined sources
Beta strandi316 – 3183Combined sources
Beta strandi320 – 3223Combined sources
Helixi330 – 34819Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2INFX-ray2.30A/B/C/D1-353[»]
ProteinModelPortaliP32395.
SMRiP32395. Positions 6-349.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32395.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni29 – 335Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CFZ. Bacteria.
COG0407. LUCA.
HOGENOMiHOG000253897.
InParanoidiP32395.
KOiK01599.
OMAiGSSKDFR.
OrthoDBiEOG6VXF6H.
PhylomeDBiP32395.

Family and domain databases

HAMAPiMF_00218. URO_D.
InterProiIPR006361. Uroporphyrinogen_deCO2ase_HemE.
IPR000257. Uroporphyrinogen_deCOase.
[Graphical view]
PfamiPF01208. URO-D. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01464. hemE. 1 hit.
PROSITEiPS00906. UROD_1. 1 hit.
PS00907. UROD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32395-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKRETFNET FLKAARGEKA DHTPVWYMRQ AGRSQPEYRK LKEKYGLFEI
60 70 80 90 100
THQPELCAYV TRLPVEQYGV DAAILYKDIM TPLPSIGVDV EIKNGIGPVI
110 120 130 140 150
DQPIRSLADI EKLGQIDPEQ DVPYVLETIK LLVNEQLNVP LIGFSGAPFT
160 170 180 190 200
LASYMIEGGP SKNYNKTKAF MYSMPDAWNL LMSKLADMII VYVKAQIEAG
210 220 230 240 250
AKAIQIFDSW VGALNQADYR TYIKPVMNRI FSELAKENVP LIMFGVGASH
260 270 280 290 300
LAGDWHDLPL DVVGLDWRLG IDEARSKGIT KTVQGNLDPS ILLAPWEVIE
310 320 330 340 350
QKTKEILDQG MESDGFIFNL GHGVFPDVSP EVLKKLTAFV HEYSQNKKMG

QYS
Length:353
Mass (Da):39,647
Last modified:October 1, 1993 - v1
Checksum:iF499C26BBAFA337E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M97208 Genomic DNA. Translation: AAA22517.1.
Y14083 Genomic DNA. Translation: CAA74518.1.
AL009126 Genomic DNA. Translation: CAB12852.1.
PIRiB47045.
RefSeqiNP_388893.1. NC_000964.3.
WP_009966929.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB12852; CAB12852; BSU10120.
GeneIDi936296.
KEGGibsu:BSU10120.
PATRICi18973720. VBIBacSub10457_1054.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M97208 Genomic DNA. Translation: AAA22517.1.
Y14083 Genomic DNA. Translation: CAA74518.1.
AL009126 Genomic DNA. Translation: CAB12852.1.
PIRiB47045.
RefSeqiNP_388893.1. NC_000964.3.
WP_009966929.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2INFX-ray2.30A/B/C/D1-353[»]
ProteinModelPortaliP32395.
SMRiP32395. Positions 6-349.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100005626.

Proteomic databases

PaxDbiP32395.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12852; CAB12852; BSU10120.
GeneIDi936296.
KEGGibsu:BSU10120.
PATRICi18973720. VBIBacSub10457_1054.

Phylogenomic databases

eggNOGiENOG4105CFZ. Bacteria.
COG0407. LUCA.
HOGENOMiHOG000253897.
InParanoidiP32395.
KOiK01599.
OMAiGSSKDFR.
OrthoDBiEOG6VXF6H.
PhylomeDBiP32395.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00321.
BioCyciBSUB:BSU10120-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP32395.

Family and domain databases

HAMAPiMF_00218. URO_D.
InterProiIPR006361. Uroporphyrinogen_deCO2ase_HemE.
IPR000257. Uroporphyrinogen_deCOase.
[Graphical view]
PfamiPF01208. URO-D. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01464. hemE. 1 hit.
PROSITEiPS00906. UROD_1. 1 hit.
PS00907. UROD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes."
    Hansson M., Hederstedt L.
    J. Bacteriol. 174:8081-8093(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus subtilis chromosome contains several dysfunctional genes, the glyB marker, many genes encoding transporter proteins, and the ubiquitous hit gene."
    Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H., Venema G., Bron S.
    Microbiology 144:859-875(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  4. "Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis."
    Fan J., Liu Q., Hao Q., Teng M., Niu L.
    J. Bacteriol. 189:3573-3580(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), FUNCTION, SUBUNIT.

Entry informationi

Entry nameiDCUP_BACSU
AccessioniPrimary (citable) accession number: P32395
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: February 17, 2016
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.