PDXA_YERPE
ID PDXA_YERPE Reviewed; 331 AA.
AC P58719; Q0WJH2;
DT 31-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 31-JAN-2002, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=4-hydroxythreonine-4-phosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00536};
DE EC=1.1.1.262 {ECO:0000255|HAMAP-Rule:MF_00536};
DE AltName: Full=4-(phosphohydroxy)-L-threonine dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00536};
GN Name=pdxA {ECO:0000255|HAMAP-Rule:MF_00536};
GN OrderedLocusNames=YPO0493, y3682, YP_3686;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
CC -!- FUNCTION: Catalyzes the NAD(P)-dependent oxidation of 4-(phosphooxy)-L-
CC threonine (HTP) into 2-amino-3-oxo-4-(phosphooxy)butyric acid which
CC spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate
CC (AHAP). {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-(phosphooxy)-L-threonine + NAD(+) = 3-amino-2-oxopropyl
CC phosphate + CO2 + NADH; Xref=Rhea:RHEA:32275, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57279, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58452; EC=1.1.1.262; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00536};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00536};
CC Note=Binds 1 divalent metal cation per subunit. Can use ions such as
CC Zn(2+), Mg(2+) or Co(2+). {ECO:0000255|HAMAP-Rule:MF_00536};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 4/5.
CC {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- MISCELLANEOUS: The active site is located at the dimer interface.
CC {ECO:0000255|HAMAP-Rule:MF_00536}.
CC -!- SIMILARITY: Belongs to the PdxA family. {ECO:0000255|HAMAP-
CC Rule:MF_00536}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM87230.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAS63834.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AL590842; CAL19173.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM87230.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE017042; AAS63834.1; ALT_INIT; Genomic_DNA.
DR PIR; AC0061; AC0061.
DR RefSeq; WP_002210489.1; NZ_WUCM01000024.1.
DR RefSeq; YP_002345566.1; NC_003143.1.
DR PDB; 3LXY; X-ray; 1.70 A; A=1-331.
DR PDBsum; 3LXY; -.
DR AlphaFoldDB; P58719; -.
DR SMR; P58719; -.
DR STRING; 214092.YPO0493; -.
DR PaxDb; P58719; -.
DR DNASU; 1148629; -.
DR EnsemblBacteria; AAM87230; AAM87230; y3682.
DR EnsemblBacteria; AAS63834; AAS63834; YP_3686.
DR GeneID; 57974117; -.
DR KEGG; ype:YPO0493; -.
DR KEGG; ypk:y3682; -.
DR KEGG; ypm:YP_3686; -.
DR PATRIC; fig|214092.21.peg.743; -.
DR eggNOG; COG1995; Bacteria.
DR HOGENOM; CLU_040168_1_0_6; -.
DR UniPathway; UPA00244; UER00312.
DR EvolutionaryTrace; P58719; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0050570; F:4-hydroxythreonine-4-phosphate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR HAMAP; MF_00536; PdxA; 1.
DR InterPro; IPR037510; PdxA.
DR InterPro; IPR005255; PdxA_fam.
DR PANTHER; PTHR30004; PTHR30004; 1.
DR Pfam; PF04166; PdxA; 1.
DR TIGRFAMs; TIGR00557; pdxA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Cytoplasm; Magnesium; Metal-binding; NAD; NADP;
KW Oxidoreductase; Pyridoxine biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..331
FT /note="4-hydroxythreonine-4-phosphate dehydrogenase"
FT /id="PRO_0000188841"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 167
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 212
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 267
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 284
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT BINDING 293
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00536"
FT STRAND 6..11
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 19..26
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 32..39
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 41..50
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 56..59
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 95..111
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 124..129
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 151..156
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 159..165
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 173..176
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 179..195
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 204..207
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 211..217
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 222..225
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 241..245
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 260..266
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 267..278
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 283..291
FT /evidence="ECO:0007829|PDB:3LXY"
FT STRAND 293..298
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 302..304
FT /evidence="ECO:0007829|PDB:3LXY"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:3LXY"
FT HELIX 313..328
FT /evidence="ECO:0007829|PDB:3LXY"
SQ SEQUENCE 331 AA; 35270 MW; 9E7675F0F7D64349 CRC64;
MHNHNNRLVI TPGEPAGVGP DLAITLAQQD WPVELVVCAD PALLLARASQ LNLPLQLREY
QADQPAIAQQ AGSLTILPVK TAVNVVPGKL DVGNSHYVVE TLAKACDGAI SGEFAALVTG
PVQKSIINDA GIPFIGHTEF FADRSHCQRV VMMLATEELR VALATTHLPL LAVPGAITQA
SLHEVITILD NDLKTKFGIT QPQIYVCGLN PHAGEGGHMG HEEIDTIIPA LNTLRQQGIN
LIGPLPADTL FQPKYLQHAD AVLAMYHDQG LPVLKYQGFG RAVNITLGLP FIRTSVDHGT
ALELAATGTA DVGSFITALN LAIKMINNSN E
