PDXS_MYCTU
ID PDXS_MYCTU Reviewed; 299 AA.
AC P9WII9; L0TCW3; O06208; P60796;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 44.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PdxS {ECO:0000255|HAMAP-Rule:MF_01824};
DE Short=PLP synthase subunit PdxS {ECO:0000255|HAMAP-Rule:MF_01824};
DE EC=4.3.3.6 {ECO:0000255|HAMAP-Rule:MF_01824};
DE AltName: Full=Pdx1 {ECO:0000255|HAMAP-Rule:MF_01824};
GN Name=pdxS {ECO:0000255|HAMAP-Rule:MF_01824}; OrderedLocusNames=Rv2606c;
GN ORFNames=MTCY1A10.27;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP PUPYLATION AT LYS-271, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=20066036; DOI=10.1371/journal.pone.0008589;
RA Festa R.A., McAllister F., Pearce M.J., Mintseris J., Burns K.E.,
RA Gygi S.P., Darwin K.H.;
RT "Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium
RT tuberculosis.";
RL PLoS ONE 5:E8589-E8589(2010).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
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 the PdxT subunit. Can also use ribulose 5-
CC phosphate and dihydroxyacetone phosphate as substrates, resulting from
CC enzyme-catalyzed isomerization of RBP and G3P, respectively.
CC {ECO:0000255|HAMAP-Rule:MF_01824}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01824};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01824}.
CC -!- SUBUNIT: In the presence of PdxT, forms a dodecamer of heterodimers.
CC {ECO:0000255|HAMAP-Rule:MF_01824}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000255|HAMAP-
CC Rule:MF_01824}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL123456; CCP45403.1; -; Genomic_DNA.
DR PIR; E70570; E70570.
DR RefSeq; NP_217122.1; NC_000962.3.
DR RefSeq; WP_003413468.1; NZ_NVQJ01000023.1.
DR PDB; 4JDY; X-ray; 1.80 A; A/B/C=11-274.
DR PDBsum; 4JDY; -.
DR AlphaFoldDB; P9WII9; -.
DR SMR; P9WII9; -.
DR STRING; 83332.Rv2606c; -.
DR PaxDb; P9WII9; -.
DR DNASU; 888592; -.
DR GeneID; 45426609; -.
DR GeneID; 888592; -.
DR KEGG; mtu:Rv2606c; -.
DR TubercuList; Rv2606c; -.
DR eggNOG; COG0214; Bacteria.
DR OMA; RYANRGW; -.
DR PhylomeDB; P9WII9; -.
DR BRENDA; 4.3.3.6; 3445.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0016843; F:amine-lyase activity; IDA:MTBBASE.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IDA:MTBBASE.
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; Isopeptide bond; Lyase; Pyridoxal phosphate;
KW Reference proteome; Schiff base; Ubl conjugation.
FT CHAIN 1..299
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxS"
FT /id="PRO_0000109405"
FT ACT_SITE 86
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 29
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 158
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 170
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 219
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT BINDING 240..241
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01824"
FT CROSSLNK 271
FT /note="Isoglutamyl lysine isopeptide (Lys-Gln) (interchain
FT with Q-Cter in protein Pup)"
FT /evidence="ECO:0000269|PubMed:20066036"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 26..32
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 33..41
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 54..60
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 69..78
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 92..101
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 130..136
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 163..181
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 187..193
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 198..207
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 211..216
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 223..231
FT /evidence="ECO:0007829|PDB:4JDY"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 241..243
FT /evidence="ECO:0007829|PDB:4JDY"
FT TURN 244..246
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 249..261
FT /evidence="ECO:0007829|PDB:4JDY"
FT TURN 262..264
FT /evidence="ECO:0007829|PDB:4JDY"
FT HELIX 266..273
FT /evidence="ECO:0007829|PDB:4JDY"
SQ SEQUENCE 299 AA; 31365 MW; 2A8B2BF5F7AF89D1 CRC64;
MDPAGNPATG TARVKRGMAE MLKGGVIMDV VTPEQARIAE GAGAVAVMAL ERVPADIRAQ
GGVSRMSDPD MIEGIIAAVT IPVMAKVRIG HFVEAQILQT LGVDYIDESE VLTPADYAHH
IDKWNFTVPF VCGATNLGEA LRRISEGAAM IRSKGEAGTG DVSNATTHMR AIGGEIRRLT
SMSEDELFVA AKELQAPYEL VAEVARAGKL PVTLFTAGGI ATPADAAMMM QLGAEGVFVG
SGIFKSGAPE HRAAAIVKAT TFFDDPDVLA KVSRGLGEAM VGINVDEIAV GHRLAQRGW
