HIS5A_ARATH
ID HIS5A_ARATH Reviewed; 270 AA.
AC P34047; Q67YN9; Q67YZ9; Q8VYM1;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Imidazoleglycerol-phosphate dehydratase 1, chloroplastic {ECO:0000303|PubMed:8066131};
DE Short=IGPD 1 {ECO:0000303|PubMed:8066131};
DE EC=4.2.1.19 {ECO:0000269|PubMed:8066131};
DE AltName: Full=Protein HISTIDINE BIOSYNTHESIS 5A {ECO:0000303|PubMed:16547652};
DE Flags: Precursor;
GN Name=HISN5A {ECO:0000303|PubMed:16547652};
GN OrderedLocusNames=At3g22425 {ECO:0000312|Araport:AT3G22425};
GN ORFNames=MCB17.17 {ECO:0000312|EMBL:BAB01781.1};
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 [MRNA] (ISOFORM 1), CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=8066131; DOI=10.1104/pp.105.2.579;
RA Tada S., Volrath S., Guyer D., Scheidegger A., Ryals J., Ohta D., Ward E.;
RT "Isolation and characterization of cDNAs encoding
RT imidazoleglycerolphosphate dehydratase from Arabidopsis thaliana.";
RL Plant Physiol. 105:579-583(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16547652; DOI=10.1007/s00726-005-0247-0;
RA Stepansky A., Leustek T.;
RT "Histidine biosynthesis in plants.";
RL Amino Acids 30:127-142(2006).
RN [9]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17434988; DOI=10.1104/pp.107.096511;
RA Muralla R., Sweeney C., Stepansky A., Leustek T., Meinke D.;
RT "Genetic dissection of histidine biosynthesis in Arabidopsis.";
RL Plant Physiol. 144:890-903(2007).
RN [10]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-63, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER CYS-62, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 64-270 IN COMPLEX WITH MANGANESE
RP IONS.
RX PubMed=16338409; DOI=10.1016/j.str.2005.08.012;
RA Glynn S.E., Baker P.J., Sedelnikova S.E., Davies C.L., Eadsforth T.C.,
RA Levy C.W., Rodgers H.F., Blackburn G.M., Hawkes T.R., Viner R., Rice D.W.;
RT "Structure and mechanism of imidazoleglycerol-phosphate dehydratase.";
RL Structure 13:1809-1817(2005).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-
CC 4-yl)-2-oxopropyl phosphate + H2O; Xref=Rhea:RHEA:11040,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:57766, ChEBI:CHEBI:58278; EC=4.2.1.19;
CC Evidence={ECO:0000269|PubMed:8066131};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16338409};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000269|PubMed:16338409};
CC -!- PATHWAY: Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine
CC from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9.
CC {ECO:0000269|PubMed:8066131}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Comment=Experimental confirmation may be lacking for some isoforms.;
CC Name=1;
CC IsoId=P34047-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P34047-2; Sequence=VSP_008895;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the imidazoleglycerol-phosphate dehydratase
CC family. {ECO:0000305}.
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DR EMBL; U02689; AAA93196.1; -; mRNA.
DR EMBL; AB022215; BAB01781.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76636.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76637.1; -; Genomic_DNA.
DR EMBL; AK118815; BAC43405.1; -; mRNA.
DR EMBL; AY070442; AAL49845.1; -; mRNA.
DR EMBL; AK176319; BAD44082.1; -; mRNA.
DR EMBL; AK176429; BAD44192.1; -; mRNA.
DR EMBL; AY087948; AAM65496.1; -; mRNA.
DR RefSeq; NP_850624.1; NM_180293.1. [P34047-2]
DR RefSeq; NP_850625.1; NM_180294.2. [P34047-1]
DR PDB; 2F1D; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=64-270.
DR PDBsum; 2F1D; -.
DR AlphaFoldDB; P34047; -.
DR SMR; P34047; -.
DR BioGRID; 7144; 1.
DR DIP; DIP-48462N; -.
DR STRING; 3702.AT3G22425.2; -.
DR iPTMnet; P34047; -.
DR PaxDb; P34047; -.
DR PRIDE; P34047; -.
DR ProteomicsDB; 230245; -. [P34047-1]
DR EnsemblPlants; AT3G22425.1; AT3G22425.1; AT3G22425. [P34047-2]
DR EnsemblPlants; AT3G22425.2; AT3G22425.2; AT3G22425. [P34047-1]
DR GeneID; 821812; -.
DR Gramene; AT3G22425.1; AT3G22425.1; AT3G22425. [P34047-2]
DR Gramene; AT3G22425.2; AT3G22425.2; AT3G22425. [P34047-1]
DR KEGG; ath:AT3G22425; -.
DR Araport; AT3G22425; -.
DR TAIR; locus:1005716545; AT3G22425.
DR eggNOG; KOG3143; Eukaryota.
DR HOGENOM; CLU_044308_1_1_1; -.
DR OMA; ARHGLFD; -.
DR PhylomeDB; P34047; -.
DR BioCyc; MetaCyc:AT3G22425-MON; -.
DR UniPathway; UPA00031; UER00011.
DR EvolutionaryTrace; P34047; -.
DR PRO; PR:P34047; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; P34047; baseline and differential.
DR Genevisible; P34047; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0004424; F:imidazoleglycerol-phosphate dehydratase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000105; P:histidine biosynthetic process; IDA:TAIR.
DR CDD; cd07914; IGPD; 1.
DR Gene3D; 3.30.230.40; -; 2.
DR HAMAP; MF_00076; HisB; 1.
DR InterPro; IPR038494; IGPD_sf.
DR InterPro; IPR000807; ImidazoleglycerolP_deHydtase.
DR InterPro; IPR020565; ImidazoleglycerP_deHydtase_CS.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR PANTHER; PTHR23133; PTHR23133; 1.
DR Pfam; PF00475; IGPD; 1.
DR SUPFAM; SSF54211; SSF54211; 2.
DR PROSITE; PS00954; IGP_DEHYDRATASE_1; 1.
DR PROSITE; PS00955; IGP_DEHYDRATASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Amino-acid biosynthesis;
KW Chloroplast; Histidine biosynthesis; Lyase; Manganese; Metal-binding;
KW Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..62
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 63..270
FT /note="Imidazoleglycerol-phosphate dehydratase 1,
FT chloroplastic"
FT /id="PRO_0000158253"
FT REGION 250..270
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 84
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 110..118
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 110
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 136..140
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 136
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 140
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 184
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 208
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 232..240
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT BINDING 232
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 233
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 236
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16338409,
FT ECO:0007744|PDB:2F1D"
FT BINDING 262..264
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O23346"
FT MOD_RES 63
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 205..270
FT /note="LVEHFFQSLVNTSGMTLHIRQLAGENSHHIIEATFKAFARALRQATETDPRR
FT GGTIPSSKGVLSRS -> VLSLLLELSSFGFICVIRCLVIIESVAKNCLTFRFVVGGAL
FT FPVVGEYFWYDSSHPAARW (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_008895"
FT CONFLICT 201
FT /note="Y -> C (in Ref. 6; BAD44082)"
FT /evidence="ECO:0000305"
FT STRAND 75..81
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 86..92
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:2F1D"
FT HELIX 106..119
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 122..128
FT /evidence="ECO:0007829|PDB:2F1D"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:2F1D"
FT HELIX 136..154
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 166..170
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 173..180
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 186..190
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:2F1D"
FT HELIX 205..217
FT /evidence="ECO:0007829|PDB:2F1D"
FT STRAND 220..227
FT /evidence="ECO:0007829|PDB:2F1D"
FT HELIX 231..250
FT /evidence="ECO:0007829|PDB:2F1D"
SQ SEQUENCE 270 AA; 29225 MW; 7132D80CC687E20C CRC64;
MELSSASAIL SHSSSAAQLL RPKLGFIDLL PRRAMIVSSP SSSLPRFLRM ESQSQLRQSI
SCSASSSSSM ALGRIGEVKR VTKETNVSVK INLDGTGVAD SSSGIPFLDH MLDQLASHGL
FDVHVRATGD VHIDDHHTNE DIALAIGTAL LKALGERKGI NRFGDFTAPL DEALIHVSLD
LSGRPYLGYN LEIPTQRVGT YDTQLVEHFF QSLVNTSGMT LHIRQLAGEN SHHIIEATFK
AFARALRQAT ETDPRRGGTI PSSKGVLSRS
