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PDX11_ARATH
ID   PDX11_ARATH             Reviewed;         309 AA.
AC   O80448;
DT   15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   03-AUG-2022, entry version 151.
DE   RecName: Full=Pyridoxal 5'-phosphate synthase subunit PDX1.1;
DE            Short=AtPDX1.1;
DE            Short=AtPDX1;2;
DE            Short=PLP synthase subunit PDX1.1;
DE            EC=4.3.3.6 {ECO:0000269|PubMed:17468224};
DE   AltName: Full=HEVER-like protein;
GN   Name=PDX11; Synonyms=PDX1L1; OrderedLocusNames=At2g38230;
GN   ORFNames=F16M14.16;
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(1999).
RN   [2]
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   [3]
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   [4]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=16157873; DOI=10.1073/pnas.0506228102;
RA   Tambasco-Studart M., Titiz O., Raschle T., Forster G., Amrhein N.,
RA   Fitzpatrick T.B.;
RT   "Vitamin B6 biosynthesis in higher plants.";
RL   Proc. Natl. Acad. Sci. U.S.A. 102:13687-13692(2005).
RN   [5]
RP   TISSUE SPECIFICITY, AND INTERACTION WITH PDX1.2; PDX1.3 AND PDX2.
RC   STRAIN=cv. C24;
RX   PubMed=16766694; DOI=10.1105/tpc.105.036269;
RA   Wagner S., Bernhardt A., Leuendorf J.E., Drewke C., Lytovchenko A.,
RA   Mujahed N., Gurgui C., Frommer W.B., Leistner E., Fernie A.R., Hellmann H.;
RT   "Analysis of the Arabidopsis rsr4-1/pdx1-3 mutant reveals the critical
RT   function of the PDX1 protein family in metabolism, development, and vitamin
RT   B6 biosynthesis.";
RL   Plant Cell 18:1722-1735(2006).
RN   [6]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=17468224; DOI=10.1104/pp.107.096784;
RA   Tambasco-Studart M., Tews I., Amrhein N., Fitzpatrick T.B.;
RT   "Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in
RT   vitamin B6 biosynthesis.";
RL   Plant Physiol. 144:915-925(2007).
CC   -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC       5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC       ammonia is provided by PDX2. Can also use ribulose 5-phosphate and
CC       dihydroxyacetone phosphate as substrates, resulting from enzyme-
CC       catalyzed isomerization of RBP and G3P, respectively. Also plays an
CC       indirect role in resistance to singlet oxygen-generating
CC       photosensitizers. {ECO:0000269|PubMed:16157873,
CC       ECO:0000269|PubMed:17468224}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC         L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC         phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC         ChEBI:CHEBI:597326; EC=4.3.3.6;
CC         Evidence={ECO:0000269|PubMed:17468224};
CC   -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC   -!- SUBUNIT: Homodimer or heterodimer with PDX1.2 or PDX1.3. Interacts with
CC       PDX2. {ECO:0000269|PubMed:16766694}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16157873}.
CC   -!- TISSUE SPECIFICITY: Expressed in flowers, shoots, leaves and weakly in
CC       roots. {ECO:0000269|PubMed:16766694}.
CC   -!- MISCELLANEOUS: Vitamin B6 is an essential quencher of singlet oxygen in
CC       plants, that can protect cellular membranes from lipid peroxidation.
CC   -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR   EMBL; AC003028; AAC27172.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09511.1; -; Genomic_DNA.
DR   EMBL; AF370296; AAK44111.1; -; mRNA.
DR   EMBL; AF385694; AAK60287.1; -; mRNA.
DR   EMBL; AY063043; AAL34217.1; -; mRNA.
DR   PIR; T01255; T01255.
DR   RefSeq; NP_181358.1; NM_129380.3.
DR   PDB; 5LNT; X-ray; 2.32 A; A/B/C/D=1-309.
DR   PDBsum; 5LNT; -.
DR   AlphaFoldDB; O80448; -.
DR   SMR; O80448; -.
DR   BioGRID; 3744; 7.
DR   IntAct; O80448; 3.
DR   STRING; 3702.AT2G38230.1; -.
DR   iPTMnet; O80448; -.
DR   PaxDb; O80448; -.
DR   PRIDE; O80448; -.
DR   ProteomicsDB; 251375; -.
DR   DNASU; 818402; -.
DR   EnsemblPlants; AT2G38230.1; AT2G38230.1; AT2G38230.
DR   GeneID; 818402; -.
DR   Gramene; AT2G38230.1; AT2G38230.1; AT2G38230.
DR   KEGG; ath:AT2G38230; -.
DR   Araport; AT2G38230; -.
DR   TAIR; locus:2042932; AT2G38230.
DR   eggNOG; KOG1606; Eukaryota.
DR   HOGENOM; CLU_055352_1_0_1; -.
DR   InParanoid; O80448; -.
DR   OMA; HYNDAHV; -.
DR   OrthoDB; 1090029at2759; -.
DR   PhylomeDB; O80448; -.
DR   BioCyc; ARA:AT2G38230-MON; -.
DR   BioCyc; MetaCyc:AT2G38230-MON; -.
DR   UniPathway; UPA00245; -.
DR   PRO; PR:O80448; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; O80448; baseline and differential.
DR   Genevisible; O80448; AT.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0005829; C:cytosol; IDA:TAIR.
DR   GO; GO:0005783; C:endoplasmic reticulum; HDA:TAIR.
DR   GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR   GO; GO:0046982; F:protein heterodimerization activity; IPI:TAIR.
DR   GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR   GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR   GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR   GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR   CDD; cd04727; pdxS; 1.
DR   Gene3D; 3.20.20.70; -; 1.
DR   HAMAP; MF_01824; PdxS; 1.
DR   InterPro; IPR013785; Aldolase_TIM.
DR   InterPro; IPR001852; PdxS/SNZ.
DR   InterPro; IPR033755; PdxS/SNZ_N.
DR   InterPro; IPR011060; RibuloseP-bd_barrel.
DR   PANTHER; PTHR31829; PTHR31829; 1.
DR   Pfam; PF01680; SOR_SNZ; 1.
DR   PIRSF; PIRSF029271; Pdx1; 1.
DR   SUPFAM; SSF51366; SSF51366; 1.
DR   TIGRFAMs; TIGR00343; TIGR00343; 1.
DR   PROSITE; PS01235; PDXS_SNZ_1; 1.
DR   PROSITE; PS51129; PDXS_SNZ_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Cytoplasm; Lyase; Pyridoxal phosphate;
KW   Reference proteome; Schiff base.
FT   CHAIN           1..309
FT                   /note="Pyridoxal 5'-phosphate synthase subunit PDX1.1"
FT                   /id="PRO_0000109366"
FT   ACT_SITE        98
FT                   /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         41
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         170
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         182
FT                   /ligand="D-glyceraldehyde 3-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:59776"
FT                   /evidence="ECO:0000250|UniProtKB:Q03148"
FT   BINDING         231
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   BINDING         252..253
FT                   /ligand="D-ribose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:78346"
FT                   /evidence="ECO:0000250|UniProtKB:O59080"
FT   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0000250|UniProtKB:Q8L940"
FT   HELIX           23..31
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           32..34
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          38..44
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           45..53
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          57..61
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           66..72
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           81..90
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          95..100
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           104..112
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          116..121
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           135..137
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          142..148
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           149..158
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          161..166
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           175..192
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           196..198
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           199..205
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           210..219
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          223..230
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           235..243
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   STRAND          247..253
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   TURN            254..257
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           261..273
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   TURN            274..276
FT                   /evidence="ECO:0007829|PDB:5LNT"
FT   HELIX           278..285
FT                   /evidence="ECO:0007829|PDB:5LNT"
SQ   SEQUENCE   309 AA;  32862 MW;  10D9EEDAEDC0BC4C CRC64;
     MAGTGVVAVY GEGAMTETKQ KSPFSVKVGL AQMLRGGVIM DVVNAEQARI AEEAGACAVM
     ALERVPADIR AQGGVARMSD PEMIKEIKNA VTIPVMAKAR IGHFVEAQIL EAIGVDYVDE
     SEVLTLADED NHINKHNFKI PFVCGCRNLG EALRRIREGA AMIRTKGEAG TGNVVEAVRH
     VRSVNGAIRL LRSMDDDEVF TYAKKIAAPY DLVVQTKELG RLPVVQFAAG GVATPADAAL
     MMQLGCDGVF VGSGVFKSGD PVKRAKAIVQ AVTNYRDAAV LAEVSCGLGE AMVGLNLDDK
     VERFASRSE
 
 
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