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Q43316 (HEM3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 124. 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, chloroplastic

Short name=PBG
EC=2.5.1.61
Alternative name(s):
Hydroxymethylbilane synthase
Short name=HMBS
Pre-uroporphyrinogen synthase
Protein RUGOSA1
Gene names
Name:HEMC
Synonyms:RUG1
Ordered Locus Names:At5g08280
ORF Names:F8L15_10
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length382 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. Ref.8

Catalytic activity

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

Cofactor

Binds 1 dipyrromethane group covalently. Ref.6

Enzyme regulation

Inhibited by NH3, heavy-metal ions, hydroxylamine and 2-bromoporphobilinogen. Not inhibited by N-ethylmaleimide. Ref.6

Pathway

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

Porphyrin-containing compound metabolism; chlorophyll biosynthesis. HAMAP-Rule MF_00260

Subunit structure

Monomer. Ref.6

Subcellular location

Plastidchloroplast HAMAP-Rule MF_00260.

Miscellaneous

The porphobilinogen subunits are added sequentialy to the dipyrromethane cofactor that is covalently attached to the enzyme. The last step of the reaction involves the hydrolysis of the bound polypyrrole chain and the release of hydroxymethylbilane.

Sequence similarities

Belongs to the HMBS family.

Biophysicochemical properties

Kinetic parameters:

KM=17 µM for porphobilinogen Ref.6

pH dependence:

Optimum pH is 7.7-8.5.

Temperature dependence:

Heat stable and fully active up to 70 degrees Celsius.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 6262Chloroplast Ref.6
Chain63 – 382320Porphobilinogen deaminase, chloroplastic HAMAP-Rule MF_00260
PRO_0000013322

Regions

Region156 – 1572Cofactor binding HAMAP-Rule MF_00260
Region200 – 2056Cofactor binding HAMAP-Rule MF_00260
Region223 – 2297Cofactor binding HAMAP-Rule MF_00260

Sites

Active site1571Proton donor/acceptor Ref.9
Binding site801Cofactor
Binding site821Cofactor

Amino acid modifications

Modified residue1231Phosphoserine Ref.7
Modified residue3161S-(dipyrrolylmethanemethyl)cysteine HAMAP-Rule MF_00260

Experimental info

Mutagenesis2461A → V in rug1; reduced growth and necrotic leaf lesions. Ref.8
Sequence conflict1571D → Y in AAM64573. Ref.5

Secondary structure

.......................................................... 382
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q43316 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: 3DB771BD4E6C9D37

FASTA38241,043
        10         20         30         40         50         60 
MDIASSSLSQ AHKVVLTRQP SSRVNTCSLG SVSAIGFSLP QISSPALGKC RRKQSSSGFV 

        70         80         90        100        110        120 
KACVAVEQKT RTAIIRIGTR GSPLALAQAY ETREKLKKKH PELVEDGAIH IEIIKTTGDK 

       130        140        150        160        170        180 
ILSQPLADIG GKGLFTKEID EALINGHIDI AVHSMKDVPT YLPEKTILPC NLPREDVRDA 

       190        200        210        220        230        240 
FICLTAATLA ELPAGSVVGT ASLRRKSQIL HKYPALHVEE NFRGNVQTRL SKLQGGKVQA 

       250        260        270        280        290        300 
TLLALAGLKR LSMTENVASI LSLDEMLPAV AQGAIGIACR TDDDKMATYL ASLNHEETRL 

       310        320        330        340        350        360 
AISCERAFLE TLDGSCRTPI AGYASKDEEG NCIFRGLVAS PDGTKVLETS RKGPYVYEDM 

       370        380 
VKMGKDAGQE LLSRAGPGFF GN 

« Hide

References

« Hide 'large scale' references
[1]"Porphobilinogen deaminase is encoded by a single gene in Arabidopsis thaliana and is targeted to the chloroplasts."
Lim S.H., Witty M., Wallace-Cook A.D.M., Ilag L.I., Smith A.G.
Plant Mol. Biol. 26:863-872(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: cv. Landsberg erecta.
[2]"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. expand/collapse author list , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[4]"Empirical analysis of transcriptional activity in the Arabidopsis genome."
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. expand/collapse author list , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[5]"Full-length cDNA from Arabidopsis thaliana."
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]"Purification and properties of porphobilinogen deaminase from Arabidopsis thaliana."
Jones R.M., Jordan P.M.
Biochem. J. 299:895-902(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 63-74, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION.
Strain: cv. Columbia.
[7]"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-123, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis."
Quesada V., Sarmiento-Manus R., Gonzalez-Bayon R., Hricova A., Ponce M.R., Micol J.L.
PLoS ONE 8:E53378-E53378(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF ALA-246.
Strain: cv. Landsberg erecta.
[9]"Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme."
Roberts A., Gill R., Hussey R.J., Mikolajek H., Erskine P.T., Cooper J.B., Wood S.P., Chrystal E.J., Shoolingin-Jordan P.M.
Acta Crystallogr. D 69:471-485(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 63-382 IN COMPLEX WITH DIPYRROMETHENONE, ACTIVE SITE, S-(DIPYRROLYLMETHANEMETHYL)CYSTEINE AT CYS-316.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X73839 Genomic DNA. Translation: CAA52061.1.
X73535 Genomic DNA. Translation: CAA51941.1.
AL392174 Genomic DNA. Translation: CAC08328.1.
CP002688 Genomic DNA. Translation: AED91277.1.
AF419614 mRNA. Translation: AAL31946.1.
AY070431 mRNA. Translation: AAL49926.1.
AY123037 mRNA. Translation: AAM67570.1.
AY087012 mRNA. Translation: AAM64573.1.
PIRS50762.
RefSeqNP_196445.1. NM_120911.3.
UniGeneAt.48996.
At.5343.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4HTGX-ray1.45A63-382[»]
ProteinModelPortalQ43316.
SMRQ43316. Positions 72-373.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-8062098.

Proteomic databases

PaxDbQ43316.
PRIDEQ43316.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G08280.1; AT5G08280.1; AT5G08280.
GeneID830724.
KEGGath:AT5G08280.

Organism-specific databases

TAIRAT5G08280.

Phylogenomic databases

eggNOGCOG0181.
HOGENOMHOG000228588.
InParanoidQ43316.
KOK01749.
OMARKSTLAC.
PhylomeDBQ43316.
ProtClustDBPLN02691.

Enzyme and pathway databases

BioCycARA:AT5G08280-MONOMER.
MetaCyc:AT5G08280-MONOMER.
UniPathwayUPA00251; UER00319.
UPA00668.

Gene expression databases

GenevestigatorQ43316.

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

PROQ43316.

Entry information

Entry nameHEM3_ARATH
AccessionPrimary (citable) accession number: Q43316
Secondary accession number(s): Q8LBT0
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant 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

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names