HEM3_ORYSJ
ID HEM3_ORYSJ Reviewed; 358 AA.
AC Q6H6D2; A0A0P0VF64; Q6H6D1;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Porphobilinogen deaminase, chloroplastic;
DE Short=PBG;
DE EC=2.5.1.61;
DE AltName: Full=Hydroxymethylbilane synthase;
DE Short=HMBS;
DE AltName: Full=Pre-uroporphyrinogen synthase;
DE Flags: Precursor;
GN Name=HEMC; OrderedLocusNames=Os02g0168800, LOC_Os02g07230;
GN ORFNames=OsJ_05540, P0669G09.15-1, P0669G09.15-2;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Tetrapolymerization of the monopyrrole PBG into the
CC hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
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 -!- COFACTOR:
CC Name=dipyrromethane; Xref=ChEBI:CHEBI:60342;
CC Note=Binds 1 dipyrromethane group covalently.;
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 -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6H6D2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6H6D2-2; Sequence=VSP_037401;
CC -!- MISCELLANEOUS: The porphobilinogen subunits are added to the
CC dipyrromethane group. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the HMBS family. {ECO:0000305}.
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DR EMBL; AP005071; BAD25717.1; -; Genomic_DNA.
DR EMBL; AP005071; BAD25718.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF07931.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS77179.1; -; Genomic_DNA.
DR EMBL; CM000139; EEE56391.1; -; Genomic_DNA.
DR EMBL; AK060914; BAG87614.1; -; mRNA.
DR EMBL; AK102265; BAG95470.1; -; mRNA.
DR RefSeq; XP_015627255.1; XM_015771769.1. [Q6H6D2-1]
DR AlphaFoldDB; Q6H6D2; -.
DR SMR; Q6H6D2; -.
DR STRING; 4530.OS02T0168800-01; -.
DR PaxDb; Q6H6D2; -.
DR PRIDE; Q6H6D2; -.
DR EnsemblPlants; Os02t0168800-01; Os02t0168800-01; Os02g0168800. [Q6H6D2-1]
DR GeneID; 4328432; -.
DR Gramene; Os02t0168800-01; Os02t0168800-01; Os02g0168800. [Q6H6D2-1]
DR KEGG; osa:4328432; -.
DR eggNOG; KOG2892; Eukaryota.
DR InParanoid; Q6H6D2; -.
DR OMA; LWQANHI; -.
DR OrthoDB; 1189095at2759; -.
DR PlantReactome; R-OSA-4827054; Tetrapyrrole biosynthesis I.
DR UniPathway; UPA00251; UER00319.
DR UniPathway; UPA00668; -.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; Q6H6D2; baseline and differential.
DR Genevisible; Q6H6D2; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0004418; F:hydroxymethylbilane synthase activity; IBA:GO_Central.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:1900865; P:chloroplast RNA modification; IEA:EnsemblPlants.
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 PIRSF; PIRSF001438; 4pyrrol_synth_OHMeBilane_synth; 1.
DR PRINTS; PR00151; PORPHBDMNASE.
DR SUPFAM; SSF54782; SSF54782; 1.
DR TIGRFAMs; TIGR00212; hemC; 1.
DR PROSITE; PS00533; PORPHOBILINOGEN_DEAM; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chlorophyll biosynthesis; Chloroplast; Plastid;
KW Porphyrin biosynthesis; Reference proteome; Signal; Transferase.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..358
FT /note="Porphobilinogen deaminase, chloroplastic"
FT /id="PRO_0000376066"
FT MOD_RES 290
FT /note="S-(dipyrrolylmethanemethyl)cysteine"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..94
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_037401"
SQ SEQUENCE 358 AA; 38397 MW; 551C55AFC7AF3943 CRC64;
MPPPPRCAAT TAHHSLLGSP TCLARPRRRC CPVRAAVAVQ AEAQAKVSLI RIGTRGSPLA
LAQAHETRDK LKAAHSELAE EGAVEIVIIK TTGDMILDKP LADIGGKGLF TKEIDDALLQ
GRIDIAVHSM KDVPTYLPEG TILPCNLPRE DVRDAFICLT ASSLAELPAG SVVGSASLRR
QSQILYKYPS LKVVNFRGNV QTRLRKLKEG DVHATLLALA GLKRLNMAET ATSVLSVDEM
LPAVAQGAIG IACRSSDDTM MNYLSSLNHE DTRLAVACER EFLSVLDGNC RTPIAAYASR
DKDGNCSFRG LLASPDGSTV YETSRTGPYD FDIMVEMGKD AGHELKAKAG PGFFDSLQ
