PDXH_MYCTU
ID PDXH_MYCTU Reviewed; 224 AA.
AC P9WIJ1; L0TBR8; O06207; P65682;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=Pyridoxine 5'-phosphate oxidase {ECO:0000303|PubMed:22110704};
DE Short=PNP oxidase {ECO:0000303|PubMed:22110704};
DE Short=PNPOx {ECO:0000303|PubMed:22110704};
DE EC=1.4.3.5 {ECO:0000255|HAMAP-Rule:MF_01629, ECO:0000269|PubMed:22110704};
DE AltName: Full=Pyridoxal 5'-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_01629};
GN Name=pdxH {ECO:0000303|PubMed:22110704}; OrderedLocusNames=Rv2607;
GN ORFNames=MTCY1A10.26c;
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 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).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND PATHWAY.
RC STRAIN=H37Rv;
RX PubMed=22110704; DOI=10.1371/journal.pone.0027643;
RA Mashalidis E.H., Mukherjee T., Sledz P., Matak-Vinkovic D., Boshoff H.,
RA Abell C., Barry C.E. III;
RT "Rv2607 from Mycobacterium tuberculosis is a pyridoxine 5'-phosphate
RT oxidase with unusual substrate specificity.";
RL PLoS ONE 6:E27643-E27643(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH FMN, AND SUBUNIT.
RX PubMed=16374842; DOI=10.1002/prot.20824;
RA Pedelacq J.-D., Rho B.-S., Kim C.-Y., Waldo G.S., Lekin T.P., Segelke B.W.,
RA Rupp B., Hung L.-W., Kim S.-I., Terwilliger T.C.;
RT "Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607)
RT from Mycobacterium tuberculosis.";
RL Proteins 62:563-569(2006).
CC -!- FUNCTION: Catalyzes the oxidation of pyridoxine 5'-phosphate (PNP) into
CC pyridoxal 5'-phosphate (PLP). Unlike many PNPOx enzymes, Rv2607 does
CC not recognize pyridoxamine 5'-phosphate (PMP) as a substrate.
CC {ECO:0000269|PubMed:22110704}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:15149, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:58589, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01629,
CC ECO:0000269|PubMed:22110704};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01629,
CC ECO:0000269|PubMed:22110704};
CC Note=Appears to bind only one FMN molecule per homodimer.
CC {ECO:0000269|PubMed:22110704};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=360 uM for pyridoxine 5'-phosphate {ECO:0000269|PubMed:22110704};
CC Note=kcat is 0.01 sec(-1). {ECO:0000269|PubMed:22110704};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_01629, ECO:0000269|PubMed:22110704}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01629,
CC ECO:0000269|PubMed:16374842, ECO:0000269|PubMed:22110704}.
CC -!- MISCELLANEOUS: The electron density for the FMN cofactor is weak in the
CC crystal structure (PDB 2A2J), which does not allow FMN to be
CC definitively placed in the M.tuberculosis PNPOx active site, but the
CC residues known to interact with FMN in the E.coli and human PNPOx
CC enzymes are found to be conserved. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the pyridoxamine 5'-phosphate oxidase family.
CC {ECO:0000255|HAMAP-Rule:MF_01629}.
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DR EMBL; AL123456; CCP45404.1; -; Genomic_DNA.
DR PIR; F70570; F70570.
DR RefSeq; NP_217123.1; NC_000962.3.
DR RefSeq; WP_003413471.1; NZ_NVQJ01000023.1.
DR PDB; 2A2J; X-ray; 2.50 A; A/B=1-224.
DR PDBsum; 2A2J; -.
DR AlphaFoldDB; P9WIJ1; -.
DR SMR; P9WIJ1; -.
DR STRING; 83332.Rv2607; -.
DR PaxDb; P9WIJ1; -.
DR DNASU; 888155; -.
DR GeneID; 45426610; -.
DR GeneID; 888155; -.
DR KEGG; mtu:Rv2607; -.
DR PATRIC; fig|83332.111.peg.2911; -.
DR TubercuList; Rv2607; -.
DR eggNOG; COG0259; Bacteria.
DR OMA; PEPNAMV; -.
DR PhylomeDB; P9WIJ1; -.
DR UniPathway; UPA01068; UER00305.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0010181; F:FMN binding; IDA:UniProtKB.
DR GO; GO:0016638; F:oxidoreductase activity, acting on the CH-NH2 group of donors; IEA:InterPro.
DR GO; GO:0016899; F:oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IDA:UniProtKB.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 2.30.110.10; -; 1.
DR HAMAP; MF_01629; PdxH; 1.
DR InterPro; IPR000659; Pyridox_Oxase.
DR InterPro; IPR019740; Pyridox_Oxase_CS.
DR InterPro; IPR011576; Pyridox_Oxase_put.
DR InterPro; IPR019576; Pyridoxamine_oxidase_dimer_C.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR PANTHER; PTHR10851; PTHR10851; 1.
DR Pfam; PF10590; PNP_phzG_C; 1.
DR Pfam; PF01243; Putative_PNPOx; 1.
DR PIRSF; PIRSF000190; Pyd_amn-ph_oxd; 1.
DR TIGRFAMs; TIGR00558; pdxH; 1.
DR PROSITE; PS01064; PYRIDOX_OXIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; Oxidoreductase; Pyridoxine biosynthesis;
KW Reference proteome.
FT CHAIN 1..224
FT /note="Pyridoxine 5'-phosphate oxidase"
FT /id="PRO_0000167723"
FT BINDING 19..22
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 76..81
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 81
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 91..92
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 98
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 120
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 142
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 155..156
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 201
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 207..209
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT BINDING 211
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01629"
FT TURN 25..27
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 34..37
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 40..54
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 62..69
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 72..84
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 87..93
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 97..104
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 107..114
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 119..129
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 132..141
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 144..152
FT /evidence="ECO:0007829|PDB:2A2J"
FT HELIX 163..176
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 188..193
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 196..202
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 210..215
FT /evidence="ECO:0007829|PDB:2A2J"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:2A2J"
SQ SEQUENCE 224 AA; 25186 MW; 66ABC0AAACE90DC1 CRC64;
MDDDAQMVAI DKDQLARMRG EYGPEKDGCG DLDFDWLDDG WLTLLRRWLN DAQRAGVSEP
NAMVLATVAD GKPVTRSVLC KILDESGVAF FTSYTSAKGE QLAVTPYASA TFPWYQLGRQ
AHVQGPVSKV STEEIFTYWS MRPRGAQLGA WASQQSRPVG SRAQLDNQLA EVTRRFADQD
QIPVPPGWGG YRIAPEIVEF WQGRENRMHN RIRVANGRLE RLQP
