Q43316 (HEM3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Porphobilinogen deaminase, chloroplastic
Short name=PBG
EC=2.5.1.61

Alternative name(s):
Hydroxymethylbilane synthase
Short name=HMBS
Pre-uroporphyrinogen synthase

Gene names

Name:	HEMC
Ordered Locus Names:	At5g08280
ORF Names:	F8L15_10

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	382 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
Catalytic activity	4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3.
Cofactor	Binds 1 dipyrromethane group covalently.
Pathway	Porphyrin metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Porphyrin biosynthesis; chlorophyll biosynthesis.
Subcellular location	Plastid › chloroplast.
Miscellaneous	The porphobilinogen subunits are added to the dipyrromethane group By similarity.
Sequence similarities	Belongs to the HMBS family.

Ontologies

Keywords
Biological process	Chlorophyll biosynthesis Porphyrin biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Molecular function	Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chlorophyll biosynthetic process Traceable author statement PubMed 8192681. Source: TAIR defense response to bacterium Inferred from expression pattern PubMed 17028151. Source: TAIR peptidyl-pyrromethane cofactor linkage Inferred from electronic annotation. Source: InterPro protoporphyrinogen IX biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	apoplast Inferred from direct assay PubMed 18538804. Source: TAIR chloroplast envelope Inferred from direct assay PubMed 12938931. Source: TAIR chloroplast stroma Inferred from direct assay PubMed 16207701PubMed 18633119PubMed 20061580. Source: TAIR
Molecular_function	hydroxymethylbilane synthase activity Inferred from direct assay PubMed 8192681. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – ?		Chloroplast Potential
	Chain	? – 382		Porphobilinogen deaminase, chloroplastic		PRO_0000013322
Amino acid modifications
	Modified residue	123	1	Phosphoserine Ref.5
	Modified residue	316	1	S-(dipyrrolylmethanemethyl)cysteine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q43316 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 3DB771BD4E6C9D37	FASTA	382	41,043
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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]	"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, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
+	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.

IPI

IPI00532138.

PIR

S50762.

RefSeq

NP_196445.1. NM_120911.3.

UniGene

At.48996.
At.5343.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4HTG	X-ray	1.45	A	63-382	[»]

ProteinModelPortal

Q43316.

SMR

Q43316. Positions 74-373.

ModBase

Search...

Proteomic databases

PaxDb

Q43316.

PRIDE

Q43316.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G08280.1; AT5G08280.1; AT5G08280.

GeneID

830724.

KEGG

ath:AT5G08280.

Organism-specific databases

TAIR

At5g08280.

Phylogenomic databases

eggNOG

COG0181.

HOGENOM

HOG000228588.

InParanoid

Q43316.

KO

K01749.

OMA

NGSCDTP.

PhylomeDB

Q43316.

ProtClustDB

PLN02691.

Enzyme and pathway databases

BioCyc

ARA:AT5G08280-MONOMER.
MetaCyc:AT5G08280-MONOMER.

UniPathway

UPA00251; UER00319.
UPA00668.

Gene expression databases

ArrayExpress

Q43316.

Genevestigator

Q43316.

GermOnline

AT5G08280. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.30.160.40. 1 hit.

InterPro

IPR000860. 4pyrrol_synth_OHMeBilane_synth.
IPR022419. Porphobilin_deaminase_cofac_BS.
IPR022417. Porphobilin_deaminase_N.
IPR022418. Porphobilinogen_deaminase_C.
[Graphical view]

PANTHER

PTHR11557. PTHR11557. 1 hit.

Pfam

PF01379. Porphobil_deam. 1 hit.
PF03900. Porphobil_deamC. 1 hit.
[Graphical view]

PIRSF

PIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.

PRINTS

PR00151. PORPHBDMNASE.

SUPFAM

SSF54782. Porphobil_deam. 1 hit.

TIGRFAMs

TIGR00212. hemC. 1 hit.

PROSITE

PS00533. PORPHOBILINOGEN_DEAM. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

HEM3_ARATH

Accession

Primary (citable) accession number: Q43316

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program