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Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin) (Reg I-binding protein 1)
PLPP_RAT Reviewed; 309 AA.
Q8VD52;
01-MAR-2004, integrated into UniProtKB/Swiss-Prot.
10-JAN-2006, sequence version 2.
28-FEB-2018, entry version 104.
RecName: Full=Pyridoxal phosphate phosphatase;
Short=PLP phosphatase;
EC=3.1.3.3 {ECO:0000250|UniProtKB:Q96GD0};
EC=3.1.3.74 {ECO:0000250|UniProtKB:Q96GD0};
AltName: Full=Chronophin;
AltName: Full=Reg I-binding protein 1;
Name=Pdxp; Synonyms=Cin, Plp, Plpp, Rbp1;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Brown Norway;
PubMed=15057822; DOI=10.1038/nature02426;
Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T.,
Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A.,
Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M.,
Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K.,
Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S.,
Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J.,
Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y.,
Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A.,
Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J.,
D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R.,
Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A.,
Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E.,
Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E.,
Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D.,
Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M.,
Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O.,
Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O.,
Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H.,
Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S.,
Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J.,
Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E.,
Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F.,
Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K.,
Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S.,
Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M.,
Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M.,
Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A.,
Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S.,
Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G.,
Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H.,
Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R.,
Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M.,
Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H.,
Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S.,
Collins F.S.;
"Genome sequence of the Brown Norway rat yields insights into
mammalian evolution.";
Nature 428:493-521(2004).
[2]
NUCLEOTIDE SEQUENCE [MRNA] OF 106-309.
STRAIN=Wistar; TISSUE=Pancreas;
Wu H., Zenilman M.E.;
"Isolation of cDNA clone from rat pancreas cDNA library by two hybrid
system, clone 13.";
Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
[3]
PROTEIN SEQUENCE OF 129-138; 141-154; 186-202 AND 236-245, AND
IDENTIFICATION BY MASS SPECTROMETRY.
STRAIN=Sprague-Dawley; TISSUE=Hippocampus;
Lubec G., Chen W.-Q.;
Submitted (APR-2007) to UniProtKB.
-!- FUNCTION: Protein serine phosphatase that dephosphorylates 'Ser-3'
in cofilin and probably also dephosphorylates phospho-serine
residues in DSTN. Regulates cofilin-dependent actin cytoskeleton
reorganization. Required for normal progress through mitosis and
normal cytokinesis. Does not dephosphorylate phospho-threonines in
LIMK1. Does not dephosphorylate peptides containing phospho-
tyrosine. Pyridoxal phosphate (PLP) phosphatase, which also
catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP)
and pyridoxamine 5'-phosphate (PMP), with order of substrate
preference PLP > PNP > PMP. {ECO:0000250|UniProtKB:Q96GD0}.
-!- CATALYTIC ACTIVITY: Pyridoxal 5'-phosphate + H(2)O = pyridoxal +
phosphate. {ECO:0000250|UniProtKB:Q96GD0}.
-!- CATALYTIC ACTIVITY: O-phospho-L(or D)-serine + H(2)O = L(or D)-
serine + phosphate. {ECO:0000250|UniProtKB:Q96GD0}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000250|UniProtKB:Q96GD0};
Note=Divalent metal ions. Mg(2+) is the most effective.
{ECO:0000250|UniProtKB:Q96GD0};
-!- SUBUNIT: Homodimer (By similarity). Interacts with REG1.
{ECO:0000250|UniProtKB:Q96GD0}.
-!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
{ECO:0000250|UniProtKB:Q96GD0}. Cytoplasm, cytoskeleton
{ECO:0000250|UniProtKB:Q96GD0}. Cell projection, ruffle membrane
{ECO:0000250|UniProtKB:Q96GD0}; Peripheral membrane protein
{ECO:0000250, ECO:0000250|UniProtKB:Q96GD0}; Cytoplasmic side
{ECO:0000250|UniProtKB:Q96GD0}. Cell projection, lamellipodium
membrane {ECO:0000250|UniProtKB:Q96GD0}; Peripheral membrane
protein {ECO:0000250|UniProtKB:Q96GD0}; Cytoplasmic side
{ECO:0000250|UniProtKB:Q96GD0}. Cell membrane
{ECO:0000250|UniProtKB:Q96GD0}; Peripheral membrane protein
{ECO:0000250|UniProtKB:Q96GD0}; Cytoplasmic side
{ECO:0000250|UniProtKB:Q96GD0}. Note=Colocalizes with the actin
cytoskeleton in membrane ruffles and lamellipodia. Diffusely
distributed throughout the cytosol during pro-metaphase and
metaphase. Detected at the dynamic cell poles during telophase.
Detected at the cleavage furrow and contractile ring during
cytokinesis. Transiently detected at the plasma membrane in late
stages of cytokinesis. Detected at the midbody.
{ECO:0000250|UniProtKB:Q96GD0}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
{ECO:0000305}.
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EMBL; AABR03056024; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AF318578; AAL37168.1; -; mRNA.
UniGene; Rn.222285; -.
ProteinModelPortal; Q8VD52; -.
SMR; Q8VD52; -.
STRING; 10116.ENSRNOP00000064092; -.
PaxDb; Q8VD52; -.
PRIDE; Q8VD52; -.
UCSC; RGD:1586212; rat.
RGD; 1586212; Pdxp.
eggNOG; KOG2882; Eukaryota.
eggNOG; COG0647; LUCA.
HOGENOM; HOG000068104; -.
HOVERGEN; HBG049429; -.
InParanoid; Q8VD52; -.
PhylomeDB; Q8VD52; -.
PRO; PR:Q8VD52; -.
Proteomes; UP000002494; Unplaced.
GO; GO:0005911; C:cell-cell junction; ISO:RGD.
GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
GO; GO:0005829; C:cytosol; ISS:UniProtKB.
GO; GO:0070062; C:extracellular exosome; ISO:RGD.
GO; GO:0031258; C:lamellipodium membrane; IEA:UniProtKB-SubCell.
GO; GO:0032587; C:ruffle membrane; IEA:UniProtKB-SubCell.
GO; GO:0019838; F:growth factor binding; IPI:RGD.
GO; GO:0031072; F:heat shock protein binding; ISO:RGD.
GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
GO; GO:0098519; F:nucleotide phosphatase activity, acting on free nucleotides; IBA:GO_Central.
GO; GO:0004721; F:phosphoprotein phosphatase activity; ISS:UniProtKB.
GO; GO:0004647; F:phosphoserine phosphatase activity; IEA:UniProtKB-EC.
GO; GO:0042803; F:protein homodimerization activity; ISO:RGD.
GO; GO:0033883; F:pyridoxal phosphatase activity; ISS:UniProtKB.
GO; GO:0031247; P:actin rod assembly; ISO:RGD.
GO; GO:0071318; P:cellular response to ATP; ISO:RGD.
GO; GO:0030836; P:positive regulation of actin filament depolymerization; ISS:UniProtKB.
GO; GO:0006470; P:protein dephosphorylation; ISS:UniProtKB.
GO; GO:0032361; P:pyridoxal phosphate catabolic process; ISS:UniProtKB.
GO; GO:0032465; P:regulation of cytokinesis; ISS:UniProtKB.
GO; GO:0007088; P:regulation of mitotic nuclear division; ISS:UniProtKB.
Gene3D; 3.40.50.1000; -; 3.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006357; HAD-SF_hydro_IIA.
InterPro; IPR023214; HAD_sf.
InterPro; IPR006349; PGP_euk.
Pfam; PF13344; Hydrolase_6; 1.
PIRSF; PIRSF000915; PGP-type_phosphatase; 1.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
TIGRFAMs; TIGR01452; PGP_euk; 1.
1: Evidence at protein level;
Cell membrane; Cell projection; Complete proteome; Cytoplasm;
Cytoskeleton; Direct protein sequencing; Hydrolase; Magnesium;
Membrane; Metal-binding; Pyridoxal phosphate; Reference proteome.
CHAIN 1 309 Pyridoxal phosphate phosphatase.
/FTId=PRO_0000068839.
REGION 58 62 Substrate binding. {ECO:0000250}.
ACT_SITE 25 25 Nucleophile. {ECO:0000250}.
ACT_SITE 27 27 Proton donor. {ECO:0000250}.
METAL 25 25 Magnesium. {ECO:0000250}.
METAL 27 27 Magnesium; via carbonyl oxygen.
{ECO:0000250}.
METAL 234 234 Magnesium. {ECO:0000250}.
BINDING 178 178 Substrate. {ECO:0000250}.
BINDING 209 209 Substrate. {ECO:0000250}.
CONFLICT 106 108 APG -> GTR (in Ref. 2). {ECO:0000305}.
SEQUENCE 309 AA; 33115 MW; E609DAA5250151C4 CRC64;
MARCERLRGA ALRDVLGQAQ GVLFDCDGVL WNGERIVPGA PELLQRLAQA GKATLFVSNN
SRRARPELAL RFARLGFTGL RAEELFSSAV CAARLLRQRL PGPPDAPGAV FVLGGEGLRA
ELRAAGLRLA GDPGDDPRVR AVLVGYDEHF SFAKLTEACA HLRDPDCLLV ATDRDPWHPL
TDGSRTPGTG SLAAAVETAS GRQALVVGKP SPYMFQCITE DFSVDPARML MVGDRLETDI
LFGHRCGMTT VLTLTGVSSL EEAQAYLAAG QHDLVPHYYV ESIADLMEGL GGLSPPPQFP
DPVDGGYRP
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Pathways :
WP1654: gamma-Hexachlorocyclohexane degradation
WP2340: Thiamine (vitamin B1) biosynthesis and salvage
WP2341: vitamin B1 (thiamin) biosynthesis and salvage pathway
WP1493: Carbon assimilation C4 pathway
WP1531: Vitamin D synthesis
WP1616: ABC transporters
WP1652: Fructose and mannose metabolism
WP1657: Glycerolipid metabolism
WP1696: Riboflavin metabolism
WP1709: Thiamine metabolism
WP2292: Chemokine signaling pathway
WP2349: vitamin B3 (niacin), NAD and NADP biosynthesis pathway
WP2353: vitamin B9 (folate) biosynthesis pathway
WP731: Sterol regulatory element binding protein related
WP76: TCA Cycle
WP1028: Pentose Phosphate Pathway
WP1049: G Protein Signaling Pathways
WP1147: Pentose Phosphate Pathway
WP1165: G Protein Signaling Pathways
WP122: Pentose Phosphate Pathway
WP1231: Pentose Phosphate Pathway
WP134: Pentose Phosphate Pathway
WP1371: G Protein Signaling Pathways
WP1438: Influenza A virus infection
WP1502: Mitochondrial biogenesis
Related Genes :
[PK PDXK SOS4 At5g37850 K18L3_10] Pyridoxal kinase (EC 2.7.1.35) (Protein SALT OVERLY SENSITIVE 4) (Pyridoxal kinase-like protein SOS4) (Pyridoxine kinase) [Cleaved into: Pyridoxal kinase, N-terminally processed]
[pdxK yfeI b2418 JW2411] Pyridoxine/pyridoxal/pyridoxamine kinase (PN/PL/PM kinase) (EC 2.7.1.35) (B6-vitamer kinase) (Pyridoxal kinase 1) (PL kinase 1)
[pdxY ydgS b1636 JW1628] Pyridoxal kinase PdxY (PL kinase) (EC 2.7.1.35) (Pyridoxal kinase 2) (PL kinase 2)
[pdxT yaaE BSU00120] Pyridoxal 5'-phosphate synthase subunit PdxT (EC 4.3.3.6) (Pdx2) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[PDX2 EMB2407 At5g60540 muf9.190] Probable pyridoxal 5'-phosphate synthase subunit PDX2 (AtPDX2) (EC 4.3.3.6) (Protein EMBRYO DEFECTIVE 2407) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[pdx2 PF11_0169] Pyridoxal 5'-phosphate synthase subunit Pdx2 (EC 4.3.3.6) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[pdxS yaaD BSU00110] Pyridoxal 5'-phosphate synthase subunit PdxS (PLP synthase subunit PdxS) (EC 4.3.3.6) (Pdx1) (Superoxide-inducible protein 7) (SOI7)
[PPOX1 PDX3 PDXH At5g49970 K9P8.11] Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic (AtPPOX1) [Includes: Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx) (Pyridoxal 5'-phosphate synthase); Probable NAD(P)HX epimerase (EC 5.1.99.6)]
[PDXK C21orf124 C21orf97 PKH PNK PRED79] Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)
[pdxH b1638 JW1630] Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx) (Pyridoxal 5'-phosphate synthase)
[SNZ1 YMR096W YM6543.03] Pyridoxal 5'-phosphate synthase subunit SNZ1 (PLP synthase subunit SNZ1) (EC 4.3.3.6) (PDX1 homolog 1) (Pdx1.1) (p35)
[PDXP CIN PLP PLPP] Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin)
[Pdxk Pkh] Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)
[Pdxp Cin Plp Plpp] Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin)
[PDX13 GIP2 PDX1L3 RSR4 At5g01410 T10O8.120] Pyridoxal 5'-phosphate synthase subunit PDX1.3 (AtPDX1.3) (AtPDX1;1) (PLP synthase subunit PDX1.3) (EC 4.3.3.6)
[PDXP CIN] Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin)
[Pdxp Cin Plp Plpp Rbp1] Pyridoxal phosphate phosphatase (PLP phosphatase) (EC 3.1.3.3) (EC 3.1.3.74) (Chronophin) (Reg I-binding protein 1)
[pdx1 PFF1025c] Pyridoxal 5'-phosphate synthase subunit Pdx1 (PLP synthase subunit Pdx1) (EC 4.3.3.6)
[yigL b3826 JW5854] Pyridoxal phosphate phosphatase YigL (EC 3.1.3.74) (PLP phosphatase) (Sugar phosphatase) (EC 3.1.3.23)
[plr1 plr SPAC9E9.11] Pyridoxal reductase (PL reductase) (PL-red) (EC 1.1.1.65)
[SNO1 YMR095C YM6543.02C] Pyridoxal 5'-phosphate synthase subunit SNO1 (EC 4.3.3.6) (PDX2 homolog 1) (Pdx2.1) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[SNO3 YFL060C] Probable pyridoxal 5'-phosphate synthase subunit SNO3 (EC 4.3.3.6) (PDX2 homolog 3) (Pdx2.3) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[PDXK PKH] Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)
[pdxT Rv2604c] Pyridoxal 5'-phosphate synthase subunit PdxT (EC 4.3.3.6) (Pdx2) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[PLPBP PROSC] Pyridoxal phosphate homeostasis protein (PLP homeostasis protein) (Proline synthase co-transcribed bacterial homolog protein) (Pyridoxal phosphate-binding protein)
[ybhA b0766 JW0749] Pyridoxal phosphate phosphatase YbhA (PLP phosphatase) (EC 3.1.3.74)
[pdx1] Pyridoxal 5'-phosphate synthase subunit Pdx1 (PLP synthase subunit Pdx1) (EC 4.3.3.6)
[pdxT yaaE TM_0472] Pyridoxal 5'-phosphate synthase subunit PdxT (EC 4.3.3.6) (Pdx2) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[SNO2 YNL334C N0285] Probable pyridoxal 5'-phosphate synthase subunit SNO2 (EC 4.3.3.6) (PDX2 homolog 2) (Pdx2.2) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)
[PDX11 PDX1L1 At2g38230 F16M14.16] Pyridoxal 5'-phosphate synthase subunit PDX1.1 (AtPDX1.1) (AtPDX1;2) (PLP synthase subunit PDX1.1) (EC 4.3.3.6) (HEVER-like protein)
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