HEM3_ARATH
ID HEM3_ARATH Reviewed; 382 AA.
AC Q43316; Q8LBT0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Porphobilinogen deaminase, chloroplastic;
DE Short=PBG;
DE EC=2.5.1.61 {ECO:0000305|PubMed:8192681};
DE AltName: Full=Hydroxymethylbilane synthase;
DE Short=HMBS;
DE AltName: Full=Pre-uroporphyrinogen synthase;
DE AltName: Full=Protein RUGOSA1;
DE Flags: Precursor;
GN Name=HEMC; Synonyms=RUG1; OrderedLocusNames=At5g08280; ORFNames=F8L15_10;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=8000000; DOI=10.1007/bf00028854;
RA Lim S.H., Witty M., Wallace-Cook A.D.M., Ilag L.I., Smith A.G.;
RT "Porphobilinogen deaminase is encoded by a single gene in Arabidopsis
RT thaliana and is targeted to the chloroplasts.";
RL Plant Mol. Biol. 26:863-872(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP PROTEIN SEQUENCE OF 63-74, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, COFACTOR, AND ACTIVITY REGULATION.
RC STRAIN=cv. Columbia;
RX PubMed=8192681; DOI=10.1042/bj2990895;
RA Jones R.M., Jordan P.M.;
RT "Purification and properties of porphobilinogen deaminase from Arabidopsis
RT thaliana.";
RL Biochem. J. 299:895-902(1994).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-123, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [8]
RP FUNCTION, AND MUTAGENESIS OF ALA-246.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=23308205; DOI=10.1371/journal.pone.0053378;
RA Quesada V., Sarmiento-Manus R., Gonzalez-Bayon R., Hricova A., Ponce M.R.,
RA Micol J.L.;
RT "PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive
RT development and causes lesions in Arabidopsis.";
RL PLoS ONE 8:E53378-E53378(2013).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 63-382 IN COMPLEX WITH
RP DIPYRROMETHENONE, ACTIVE SITE, AND PROSTHETIC GROUP AT CYS-316.
RX PubMed=23519422; DOI=10.1107/s0907444912052134;
RA Roberts A., Gill R., Hussey R.J., Mikolajek H., Erskine P.T., Cooper J.B.,
RA Wood S.P., Chrystal E.J., Shoolingin-Jordan P.M.;
RT "Insights into the mechanism of pyrrole polymerization catalysed by
RT porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis
RT thaliana enzyme.";
RL Acta Crystallogr. D 69:471-485(2013).
CC -!- FUNCTION: Tetrapolymerization of the monopyrrole PBG into the
CC hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
CC {ECO:0000269|PubMed:23308205, ECO:0000269|PubMed:8192681}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+);
CC Xref=Rhea:RHEA:13185, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:57845, ChEBI:CHEBI:58126; EC=2.5.1.61;
CC Evidence={ECO:0000305|PubMed:8192681};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13186;
CC Evidence={ECO:0000305|PubMed:8192681};
CC -!- COFACTOR:
CC Name=dipyrromethane; Xref=ChEBI:CHEBI:60342;
CC Evidence={ECO:0000269|PubMed:8192681};
CC Note=Binds 1 dipyrromethane group covalently.
CC {ECO:0000269|PubMed:8192681};
CC -!- ACTIVITY REGULATION: Inhibited by NH(3), heavy-metal ions,
CC hydroxylamine and 2-bromoporphobilinogen. Not inhibited by N-
CC ethylmaleimide. {ECO:0000269|PubMed:8192681}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17 uM for porphobilinogen {ECO:0000269|PubMed:8192681};
CC pH dependence:
CC Optimum pH is 7.7-8.5.;
CC Temperature dependence:
CC Heat stable and fully active up to 70 degrees Celsius.;
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4.
CC -!- PATHWAY: Porphyrin-containing compound metabolism; chlorophyll
CC biosynthesis.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23519422,
CC ECO:0000269|PubMed:8192681}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- MISCELLANEOUS: The porphobilinogen subunits are added sequentially to
CC the dipyrromethane cofactor that is covalently attached to the enzyme.
CC The last step of the reaction involves the hydrolysis of the bound
CC polypyrrole chain and the release of hydroxymethylbilane.
CC -!- SIMILARITY: Belongs to the HMBS family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X73839; CAA52061.1; -; Genomic_DNA.
DR EMBL; X73535; CAA51941.1; -; Genomic_DNA.
DR EMBL; AL392174; CAC08328.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91277.1; -; Genomic_DNA.
DR EMBL; AF419614; AAL31946.1; -; mRNA.
DR EMBL; AY070431; AAL49926.1; -; mRNA.
DR EMBL; AY123037; AAM67570.1; -; mRNA.
DR EMBL; AY087012; AAM64573.1; -; mRNA.
DR PIR; S50762; S50762.
DR RefSeq; NP_196445.1; NM_120911.4.
DR PDB; 4HTG; X-ray; 1.45 A; A=63-382.
DR PDBsum; 4HTG; -.
DR AlphaFoldDB; Q43316; -.
DR SMR; Q43316; -.
DR BioGRID; 16002; 4.
DR STRING; 3702.AT5G08280.1; -.
DR iPTMnet; Q43316; -.
DR MetOSite; Q43316; -.
DR PaxDb; Q43316; -.
DR PRIDE; Q43316; -.
DR ProteomicsDB; 232214; -.
DR EnsemblPlants; AT5G08280.1; AT5G08280.1; AT5G08280.
DR GeneID; 830724; -.
DR Gramene; AT5G08280.1; AT5G08280.1; AT5G08280.
DR KEGG; ath:AT5G08280; -.
DR Araport; AT5G08280; -.
DR TAIR; locus:2150758; AT5G08280.
DR eggNOG; KOG2892; Eukaryota.
DR HOGENOM; CLU_019704_1_2_1; -.
DR InParanoid; Q43316; -.
DR OMA; NAHEWAG; -.
DR OrthoDB; 1189095at2759; -.
DR PhylomeDB; Q43316; -.
DR BioCyc; ARA:AT5G08280-MON; -.
DR BioCyc; MetaCyc:AT5G08280-MON; -.
DR BRENDA; 2.5.1.61; 399.
DR UniPathway; UPA00251; UER00319.
DR UniPathway; UPA00668; -.
DR PRO; PR:Q43316; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q43316; baseline and differential.
DR Genevisible; Q43316; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0004418; F:hydroxymethylbilane synthase activity; IDA:TAIR.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; TAS:TAIR.
DR GO; GO:1900865; P:chloroplast RNA modification; IMP:TAIR.
DR GO; GO:0006783; P:heme biosynthetic process; IBA:GO_Central.
DR GO; GO:0018160; P:peptidyl-pyrromethane cofactor linkage; IEA:InterPro.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.160.40; -; 1.
DR HAMAP; MF_00260; Porphobil_deam; 1.
DR InterPro; IPR000860; HemC.
DR InterPro; IPR022419; Porphobilin_deaminase_cofac_BS.
DR InterPro; IPR022417; Porphobilin_deaminase_N.
DR InterPro; IPR022418; Porphobilinogen_deaminase_C.
DR InterPro; IPR036803; Porphobilinogen_deaminase_C_sf.
DR PANTHER; PTHR11557; PTHR11557; 1.
DR Pfam; PF01379; Porphobil_deam; 1.
DR Pfam; PF03900; Porphobil_deamC; 1.
DR PRINTS; PR00151; PORPHBDMNASE.
DR SUPFAM; SSF54782; SSF54782; 1.
DR TIGRFAMs; TIGR00212; hemC; 1.
DR PROSITE; PS00533; PORPHOBILINOGEN_DEAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chlorophyll biosynthesis; Chloroplast;
KW Direct protein sequencing; Phosphoprotein; Plastid; Porphyrin biosynthesis;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..62
FT /note="Chloroplast"
FT /evidence="ECO:0000269|PubMed:8192681"
FT CHAIN 63..382
FT /note="Porphobilinogen deaminase, chloroplastic"
FT /id="PRO_0000013322"
FT ACT_SITE 157
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000269|PubMed:23519422"
FT BINDING 80
FT /ligand="dipyrromethane"
FT /ligand_id="ChEBI:CHEBI:60342"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT BINDING 82
FT /ligand="dipyrromethane"
FT /ligand_id="ChEBI:CHEBI:60342"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT BINDING 156..157
FT /ligand="dipyrromethane"
FT /ligand_id="ChEBI:CHEBI:60342"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT BINDING 200..206
FT /ligand="dipyrromethane"
FT /ligand_id="ChEBI:CHEBI:60342"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT BINDING 223..229
FT /ligand="dipyrromethane"
FT /ligand_id="ChEBI:CHEBI:60342"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT MOD_RES 123
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 316
FT /note="S-(dipyrrolylmethanemethyl)cysteine"
FT /evidence="ECO:0000305|PubMed:23519422,
FT ECO:0007744|PDB:4HTG"
FT MUTAGEN 246
FT /note="A->V: In rug1; reduced growth and necrotic leaf
FT lesions."
FT /evidence="ECO:0000269|PubMed:23308205"
FT CONFLICT 157
FT /note="D -> Y (in Ref. 5; AAM64573)"
FT /evidence="ECO:0000305"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 83..99
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 108..113
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:4HTG"
FT TURN 134..136
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 137..144
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 166..171
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 203..212
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 216..219
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 226..234
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 237..244
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 245..251
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 254..256
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:4HTG"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:4HTG"
FT TURN 270..273
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 275..280
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 284..291
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 296..311
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 318..326
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 330..339
FT /evidence="ECO:0007829|PDB:4HTG"
FT STRAND 346..355
FT /evidence="ECO:0007829|PDB:4HTG"
FT HELIX 357..372
FT /evidence="ECO:0007829|PDB:4HTG"
SQ SEQUENCE 382 AA; 41043 MW; 3DB771BD4E6C9D37 CRC64;
MDIASSSLSQ AHKVVLTRQP SSRVNTCSLG SVSAIGFSLP QISSPALGKC RRKQSSSGFV
KACVAVEQKT RTAIIRIGTR GSPLALAQAY ETREKLKKKH PELVEDGAIH IEIIKTTGDK
ILSQPLADIG GKGLFTKEID EALINGHIDI AVHSMKDVPT YLPEKTILPC NLPREDVRDA
FICLTAATLA ELPAGSVVGT ASLRRKSQIL HKYPALHVEE NFRGNVQTRL SKLQGGKVQA
TLLALAGLKR LSMTENVASI LSLDEMLPAV AQGAIGIACR TDDDKMATYL ASLNHEETRL
AISCERAFLE TLDGSCRTPI AGYASKDEEG NCIFRGLVAS PDGTKVLETS RKGPYVYEDM
VKMGKDAGQE LLSRAGPGFF GN
