MTND_KLEOX
ID MTND_KLEOX Reviewed; 180 AA.
AC Q9ZFE7; Q48390;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-JAN-2009, sequence version 2.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Acireductone dioxygenase;
DE AltName: Full=1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase;
DE Short=DHK-MTPene dioxygenase;
DE AltName: Full=Acireductone dioxygenase (Fe(2+)-requiring);
DE Short=ARD';
DE Short=Fe-ARD;
DE EC=1.13.11.54;
DE AltName: Full=Acireductone dioxygenase (Ni(2+)-requiring);
DE Short=ARD;
DE Short=Ni-ARD;
DE EC=1.13.11.53;
GN Name=mtnD; Synonyms=masB;
OS Klebsiella oxytoca.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX NCBI_TaxID=571;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-82.
RC STRAIN=M5a1;
RX PubMed=8227040; DOI=10.1016/s0021-9258(19)74534-7;
RA Balakrishnan R., Frohlich M., Rahaim P.T., Backman K., Yocum R.R.;
RT "Appendix. Cloning and sequence of the gene encoding enzyme E-1 from the
RT methionine salvage pathway of Klebsiella oxytoca.";
RL J. Biol. Chem. 268:24792-24795(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 2-180, PROTEIN SEQUENCE OF N-TERMINUS,
RP MASS SPECTROMETRY, AND COFACTOR.
RC STRAIN=UNF932;
RX PubMed=9880484; DOI=10.1074/jbc.274.3.1193;
RA Dai Y., Wensink P.C., Abeles R.H.;
RT "One protein, two enzymes.";
RL J. Biol. Chem. 274:1193-1195(1999).
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=8407993; DOI=10.1016/s0021-9258(20)80559-6;
RA Wray J.W., Abeles R.H.;
RT "A bacterial enzyme that catalyzes formation of carbon monoxide.";
RL J. Biol. Chem. 268:21466-21469(1993).
RN [4]
RP MASS SPECTROMETRY, SUBUNIT, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=11371200; DOI=10.1021/bi010110y;
RA Dai Y., Pochapsky T.C., Abeles R.H.;
RT "Mechanistic studies of two dioxygenases in the methionine salvage pathway
RT of Klebsiella pneumoniae.";
RL Biochemistry 40:6379-6387(2001).
RN [5]
RP MUTAGENESIS OF GLU-96; HIS-97; HIS-99; GLU-101; ASP-102; GLU-103 AND
RP HIS-141, AND COFACTOR.
RX PubMed=18237192; DOI=10.1021/bi7004152;
RA Chai S.C., Ju T., Dang M., Goldsmith R.B., Maroney M.J., Pochapsky T.C.;
RT "Characterization of metal binding in the active sites of acireductone
RT dioxygenase isoforms from Klebsiella ATCC 8724.";
RL Biochemistry 47:2428-2438(2008).
RN [6]
RP STRUCTURE BY NMR, SUBUNIT, AND COFACTOR.
RX PubMed=12402029; DOI=10.1038/nsb863;
RA Pochapsky T.C., Pochapsky S.S., Ju T., Mo H., Al-Mjeni F., Maroney M.J.;
RT "Modeling and experiment yields the structure of acireductone dioxygenase
RT from Klebsiella pneumoniae.";
RL Nat. Struct. Biol. 9:966-972(2002).
RN [7] {ECO:0007744|PDB:1ZRR}
RP STRUCTURE BY NMR IN COMPLEX WITH NI(2+).
RX PubMed=16518698; DOI=10.1007/s10858-005-5735-8;
RA Pochapsky T.C., Pochapsky S.S., Ju T., Hoefler C., Liang J.;
RT "A refined model for the structure of acireductone dioxygenase from
RT Klebsiella ATCC 8724 incorporating residual dipolar couplings.";
RL J. Biomol. NMR 34:117-127(2006).
RN [8] {ECO:0007744|PDB:2HJI}
RP STRUCTURE BY NMR IN COMPLEX WITH FE(2+), AND SUBUNIT.
RX PubMed=16989860; DOI=10.1016/j.jmb.2006.08.060;
RA Ju T., Goldsmith R.B., Chai S.C., Maroney M.J., Pochapsky S.S.,
RA Pochapsky T.C.;
RT "One protein, two enzymes revisited: a structural entropy switch
RT interconverts the two isoforms of acireductone dioxygenase.";
RL J. Mol. Biol. 363:823-834(2006).
CC -!- FUNCTION: Catalyzes 2 different reactions between oxygen and the
CC acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene)
CC depending upon the metal bound in the active site. Fe-containing
CC acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-
CC methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine
CC in the methionine recycle pathway. Ni-containing acireductone
CC dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and
CC formate, and does not lie on the methionine recycle pathway.
CC {ECO:0000269|PubMed:8407993}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 3-
CC (methylsulfanyl)propanoate + CO + formate + 2 H(+);
CC Xref=Rhea:RHEA:14161, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:17245, ChEBI:CHEBI:49016,
CC ChEBI:CHEBI:49252; EC=1.13.11.53;
CC Evidence={ECO:0000269|PubMed:8407993};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 4-
CC methylsulfanyl-2-oxobutanoate + formate + 2 H(+);
CC Xref=Rhea:RHEA:24504, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:16723, ChEBI:CHEBI:49252;
CC EC=1.13.11.54; Evidence={ECO:0000269|PubMed:8407993};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Fe(2+) ion per monomer. Can be replaced by Mg(2+), but
CC with lower activity.;
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Note=Binds 1 nickel ion per monomer. Can be replaced by manganese or
CC cobalt ions.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=50 uM for 1,2-dihydroxy-3-keto-1-hexene (with Ni-ARD)
CC {ECO:0000269|PubMed:11371200};
CC KM=52 uM for 1,2-dihydroxy-3-keto-1-hexene (with Fe-ARD)
CC {ECO:0000269|PubMed:11371200};
CC KM=47 uM for oxygen (with Fe-ARD) {ECO:0000269|PubMed:11371200};
CC KM=110 uM for oxygen (with Ni-ARD) {ECO:0000269|PubMed:11371200};
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via salvage
CC pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate:
CC step 5/6.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11371200,
CC ECO:0000269|PubMed:12402029, ECO:0000269|PubMed:16989860}.
CC -!- MASS SPECTROMETRY: Mass=20252; Method=Electrospray; Note=Ni-ARD.;
CC Evidence={ECO:0000269|PubMed:11371200, ECO:0000269|PubMed:9880484};
CC -!- MASS SPECTROMETRY: Mass=20238; Method=Electrospray; Note=Fe-ARD.;
CC Evidence={ECO:0000269|PubMed:9880484};
CC -!- MASS SPECTROMETRY: Mass=20236; Method=Electrospray; Note=Fe-ARD.;
CC Evidence={ECO:0000269|PubMed:11371200};
CC -!- SIMILARITY: Belongs to the acireductone dioxygenase (ARD) family.
CC {ECO:0000305}.
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DR EMBL; U00148; AAC43184.1; -; Genomic_DNA.
DR EMBL; AF102514; AAD11793.1; -; Genomic_DNA.
DR PIR; A59159; A59159.
DR RefSeq; WP_004135399.1; NZ_QDDU01000010.1.
DR PDB; 1ZRR; NMR; -; A=2-180.
DR PDB; 2HJI; NMR; -; A=2-180.
DR PDBsum; 1ZRR; -.
DR PDBsum; 2HJI; -.
DR AlphaFoldDB; Q9ZFE7; -.
DR BMRB; Q9ZFE7; -.
DR SMR; Q9ZFE7; -.
DR STRING; 571.MC52_16260; -.
DR KEGG; ag:AAD11793; -.
DR eggNOG; COG1791; Bacteria.
DR BioCyc; MetaCyc:MON-1323; -.
DR BRENDA; 1.13.11.53; 2811.
DR BRENDA; 1.13.11.54; 2811.
DR SABIO-RK; Q9ZFE7; -.
DR UniPathway; UPA00904; UER00878.
DR EvolutionaryTrace; Q9ZFE7; -.
DR GO; GO:0010308; F:acireductone dioxygenase (Ni2+-requiring) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0010309; F:acireductone dioxygenase [iron(II)-requiring] activity; IEA:UniProtKB-UniRule.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016151; F:nickel cation binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019509; P:L-methionine salvage from methylthioadenosine; IEA:UniProtKB-UniPathway.
DR GO; GO:0019284; P:L-methionine salvage from S-adenosylmethionine; IEA:UniProtKB-UniRule.
DR CDD; cd02232; cupin_ARD; 1.
DR Gene3D; 2.60.120.10; -; 1.
DR HAMAP; MF_01682; Salvage_MtnD; 1.
DR InterPro; IPR004313; ARD.
DR InterPro; IPR023956; ARD_bac.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR PANTHER; PTHR23418; PTHR23418; 1.
DR Pfam; PF03079; ARD; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Dioxygenase;
KW Direct protein sequencing; Iron; Metal-binding; Methionine biosynthesis;
KW Nickel; Oxidoreductase.
FT CHAIN 1..180
FT /note="Acireductone dioxygenase"
FT /id="PRO_0000359200"
FT BINDING 97
FT /ligand="Fe(2+)"
FT /ligand_id="ChEBI:CHEBI:29033"
FT /evidence="ECO:0000269|PubMed:16989860,
FT ECO:0007744|PDB:2HJI"
FT BINDING 97
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:16518698,
FT ECO:0007744|PDB:1ZRR"
FT BINDING 99
FT /ligand="Fe(2+)"
FT /ligand_id="ChEBI:CHEBI:29033"
FT /evidence="ECO:0000269|PubMed:16989860,
FT ECO:0007744|PDB:2HJI"
FT BINDING 99
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:16518698,
FT ECO:0007744|PDB:1ZRR"
FT BINDING 103
FT /ligand="Fe(2+)"
FT /ligand_id="ChEBI:CHEBI:29033"
FT /evidence="ECO:0000269|PubMed:16989860,
FT ECO:0007744|PDB:2HJI"
FT BINDING 103
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:16518698,
FT ECO:0007744|PDB:1ZRR"
FT BINDING 141
FT /ligand="Fe(2+)"
FT /ligand_id="ChEBI:CHEBI:29033"
FT /evidence="ECO:0000269|PubMed:16989860,
FT ECO:0007744|PDB:2HJI"
FT BINDING 141
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:16518698,
FT ECO:0007744|PDB:1ZRR"
FT SITE 96
FT /note="May play a role in metal incorporation in vivo"
FT SITE 102
FT /note="May play a role in transmitting local conformational
FT changes"
FT SITE 105
FT /note="Important to generate the dianion"
FT MUTAGEN 96
FT /note="E->A: Loss of dioxygenase activity and decrease in
FT expression of soluble protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 97
FT /note="H->A: Loss of dioxygenase activity and strong
FT decrease in expression of soluble protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 99
FT /note="H->A: Loss of dioxygenase activity and decrease in
FT expression of soluble protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 99
FT /note="H->S: Loss of dioxygenase activity, and little
FT affinity for either Ni(2+) or Fe(2+) ions."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 101
FT /note="E->A: Strong decrease in dioxygenase activity.
FT Exhibits high affinity for both Ni(2+) and Fe(2+) ions, but
FT the activities of both Ni(2+)- and Fe(2+)-reconstituted
FT mutant are considerably lower than wild-type enzymes."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 102
FT /note="D->A: Shows a slight decrease in dioxygenase
FT activity and high affinity for both Ni(2+) and Fe(2+)
FT ions."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 103
FT /note="E->A: Loss of dioxygenase activity and strong
FT decrease in expression of soluble protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 141
FT /note="H->A: No expression of soluble protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT MUTAGEN 141
FT /note="H->F: Strong decrease in expression of soluble
FT protein."
FT /evidence="ECO:0000269|PubMed:18237192"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:2HJI"
FT STRAND 15..19
FT /evidence="ECO:0007829|PDB:1ZRR"
FT HELIX 23..31
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:2HJI"
FT HELIX 51..69
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 72..77
FT /evidence="ECO:0007829|PDB:1ZRR"
FT HELIX 85..94
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 103..110
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:2HJI"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:1ZRR"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:1ZRR"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:1ZRR"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:1ZRR"
SQ SEQUENCE 180 AA; 20329 MW; 7EC4B7E668C91F14 CRC64;
MSALTIFSVK DPQNSLWHST NAEEIQQQLN AKGVRFERWQ ADRDLGAAPT AETVIAAYQH
AIDKLVAEKG YQSWDVISLR ADNPQKEALR EKFLNEHTHG EDEVRFFVEG AGLFCLHIGD
EVFQVLCEKN DLISVPAHTP HWFDMGSEPN FTAIRIFDNP EGWIAQFTGD DIASAYPRLA
