PDLA_RHILO
ID PDLA_RHILO Reviewed; 268 AA.
AC Q988B9;
DT 11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=4-pyridoxolactonase {ECO:0000312|EMBL:BAE53392.1};
DE EC=3.1.1.27;
GN OrderedLocusNames=mlr6805;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1] {ECO:0000305, ECO:0000312|EMBL:BAE53392.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-10,
RP IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, COFACTOR, AND SUBUNIT.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099 {ECO:0000269|PubMed:16226926};
RX PubMed=16226926; DOI=10.1016/j.bbapap.2005.08.026;
RA Funami J., Yoshikane Y., Kobayashi H., Yokochi N., Yuan B., Iwasaki K.,
RA Ohnishi K., Yagi T.;
RT "4-Pyridoxolactonase from a symbiotic nitrogen-fixing bacterium
RT Mesorhizobium loti: cloning, expression, and characterization.";
RL Biochim. Biophys. Acta 1753:234-239(2005).
RN [2] {ECO:0000312|EMBL:BAB53031.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS) IN COMPLEX WITH ZINC, CATALYTIC
RP ACTIVITY, FUNCTION, AND COFACTOR.
RX PubMed=24699732; DOI=10.1107/s2053230x14003926;
RA Kobayashi J., Yoshikane Y., Yagi T., Baba S., Mizutani K., Takahashi N.,
RA Mikami B.;
RT "Structure of 4-pyridoxolactonase from Mesorhizobium loti.";
RL Acta Crystallogr. F 70:424-432(2014).
CC -!- FUNCTION: Involved in the degradation of pyridoxine or pyridoxamine
CC (free, phosphate-unbound, forms of vitamin B6). Hydrolyzes 4-
CC pyridoxolactone to 4-pyridoxic acid. Has lower activity toward N-
CC hexanoyl-D,L-homoserine lactone, but is not active toward 5-
CC pyridoxolactone and gamma-butyrolactone. {ECO:0000269|PubMed:16226926,
CC ECO:0000269|PubMed:24699732}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-pyridoxolactone + H2O = 4-pyridoxate + H(+);
CC Xref=Rhea:RHEA:14301, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16871, ChEBI:CHEBI:30959; EC=3.1.1.27;
CC Evidence={ECO:0000269|PubMed:16226926, ECO:0000269|PubMed:24699732};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16226926, ECO:0000269|PubMed:24699732};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000269|PubMed:16226926,
CC ECO:0000269|PubMed:24699732};
CC -!- ACTIVITY REGULATION: Inhibited by Hg(2+).
CC {ECO:0000269|PubMed:16226926}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.98 uM for 4-pyridoxolactone {ECO:0000269|PubMed:16226926};
CC KM=319 uM for 4-pyridoxic acid {ECO:0000269|PubMed:16226926};
CC pH dependence:
CC Optimum pH is 7.5. Retains 36% of maximum activity at pH 5.0 and 10%
CC of maximum activity at pH 9.5. {ECO:0000269|PubMed:16226926};
CC Temperature dependence:
CC Optimum temperature is 60-70 degrees Celsius. Stable for 10 minutes
CC at 50 degrees Celsius or lower, 64% of activity remains following 10
CC minutes incubation at 55 degrees Celsius and 14% of activity remains
CC following 10 minutes incubation at 60 degrees Celsius.
CC {ECO:0000269|PubMed:16226926};
CC -!- PATHWAY: Cofactor degradation; B6 vitamer degradation; 4-pyridoxate
CC from pyridoxal: step 2/2. {ECO:0000269|PubMed:16226926}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16226926,
CC ECO:0000269|PubMed:24699732}.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily.
CC {ECO:0000305}.
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DR EMBL; AB197037; BAE53392.1; -; Genomic_DNA.
DR EMBL; BA000012; BAB53031.1; -; Genomic_DNA.
DR RefSeq; WP_010914341.1; NC_002678.2.
DR PDB; 3AJ3; X-ray; 1.58 A; A=1-268.
DR PDB; 4KEP; X-ray; 1.83 A; A=1-268.
DR PDB; 4KEQ; X-ray; 2.28 A; A=1-268.
DR PDBsum; 3AJ3; -.
DR PDBsum; 4KEP; -.
DR PDBsum; 4KEQ; -.
DR AlphaFoldDB; Q988B9; -.
DR SMR; Q988B9; -.
DR STRING; 266835.14026434; -.
DR EnsemblBacteria; BAB53031; BAB53031; BAB53031.
DR GeneID; 66685748; -.
DR KEGG; mlo:mlr6805; -.
DR eggNOG; COG0491; Bacteria.
DR HOGENOM; CLU_030571_3_2_5; -.
DR OMA; YSILIEH; -.
DR OrthoDB; 1815576at2; -.
DR BioCyc; MetaCyc:MON-13149; -.
DR BRENDA; 3.1.1.27; 3243.
DR UniPathway; UPA00192; UER00589.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0047585; F:4-pyridoxolactonase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042820; P:vitamin B6 catabolic process; IDA:UniProtKB.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR Pfam; PF00753; Lactamase_B; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Metal-binding; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:16226926"
FT CHAIN 2..268
FT /note="4-pyridoxolactonase"
FT /evidence="ECO:0000269|PubMed:16226926"
FT /id="PRO_0000403057"
FT ACT_SITE 100
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255"
FT BINDING 96
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 185
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 207
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 207
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT BINDING 252
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24699732"
FT STRAND 5..17
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 18..21
FT /evidence="ECO:0007829|PDB:3AJ3"
FT TURN 22..25
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 29..42
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 55..61
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 75..81
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:3AJ3"
FT TURN 102..104
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 119..124
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:3AJ3"
FT TURN 131..134
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 141..147
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:4KEP"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 169..174
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 212..217
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 227..244
FT /evidence="ECO:0007829|PDB:3AJ3"
FT STRAND 247..252
FT /evidence="ECO:0007829|PDB:3AJ3"
FT HELIX 254..257
FT /evidence="ECO:0007829|PDB:3AJ3"
SQ SEQUENCE 268 AA; 29856 MW; AC209337C4609D5C CRC64;
MSDTKVYLLD GGSLVLDGYH VFWNRGPGGE VRFPVYSILI EHAEGRFLID TGYDYDHVMK
VLPFEKPIQE KHQTIPGALG LLGLEPRDID VVVNSHFHFD HCGGNKYFPH AKKICHRSEV
PQACNPQPFE HLGYSDLSFS AEAAEARGAT AQLLEGTTRA NSTFEGIDGD VDLARGVKLI
STPGHSIGHY SLLVEFPRRK PILFTIDAAY TQKSLETLCQ AAFHIDPVAG VNSMRKVKKL
AEDHGAELMY SHDMDNFKTY RTGTQFYG
