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Protein/nucleic acid deglycase 2 (EC 3.1.2.-) (EC 3.5.1.-) (EC 3.5.1.124) (Maillard deglycase)

 YHBO_ECOLI              Reviewed;         172 AA.
P45470; Q2M957;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
30-MAY-2000, sequence version 2.
18-JUL-2018, entry version 136.
RecName: Full=Protein/nucleic acid deglycase 2 {ECO:0000305|PubMed:26774339, ECO:0000305|PubMed:28596309};
EC=3.1.2.- {ECO:0000305|PubMed:26774339};
EC=3.5.1.- {ECO:0000269|PubMed:28596309};
EC=3.5.1.124 {ECO:0000305|PubMed:26774339};
AltName: Full=Maillard deglycase {ECO:0000303|PubMed:28596309};
Name=yhbO; OrderedLocusNames=b3153, JW5529;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[3]
PROTEIN SEQUENCE OF 2-9, SUBUNIT, AND SUBCELLULAR LOCATION.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=16380269; DOI=10.1016/j.pep.2005.11.011;
Abdallah J., Kern R., Malki A., Eckey V., Richarme G.;
"Cloning, expression, and purification of the general stress protein
YhbO from Escherichia coli.";
Protein Expr. Purif. 47:455-460(2006).
[4]
FUNCTION IN STRESS RESISTANCE, DISRUPTION PHENOTYPE, AND MUTAGENESIS
OF CYS-104.
PubMed=17933887; DOI=10.1128/JB.01208-07;
Abdallah J., Caldas T., Kthiri F., Kern R., Richarme G.;
"YhbO protects cells against multiple stresses.";
J. Bacteriol. 189:9140-9144(2007).
[5]
FUNCTION AS A PROTEIN DEGLYCASE, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=26774339; DOI=10.1016/j.bbrc.2016.01.068;
Abdallah J., Mihoub M., Gautier V., Richarme G.;
"The DJ-1 superfamily members YhbO and YajL from Escherichia coli
repair proteins from glycation by methylglyoxal and glyoxal.";
Biochem. Biophys. Res. Commun. 470:282-286(2016).
[6]
FUNCTION.
PubMed=27530919; DOI=10.1016/j.bbrc.2016.08.077;
Richarme G., Marguet E., Forterre P., Ishino S., Ishino Y.;
"DJ-1 family Maillard deglycases prevent acrylamide formation.";
Biochem. Biophys. Res. Commun. 478:1111-1116(2016).
[7]
FUNCTION AS A GLYOXALASE, BIOPHYSICOCHEMICAL PROPERTIES, AND ENZYME
REGULATION.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=26678554; DOI=10.1093/femsle/fnv239;
Lee C., Lee J., Lee J.Y., Park C.;
"Characterization of the Escherichia coli YajL, YhbO and ElbB
glyoxalases.";
FEMS Microbiol. Lett. 363:0-0(2016).
[8]
FUNCTION AS A NUCLEOTIDE DEGLYCASE, CATALYTIC ACTIVITY, AND DISRUPTION
PHENOTYPE.
STRAIN=K12 / BW25113;
PubMed=28596309; DOI=10.1126/science.aag1095;
Richarme G., Liu C., Mihoub M., Abdallah J., Leger T., Joly N.,
Liebart J.C., Jurkunas U.V., Nadal M., Bouloc P., Dairou J.,
Lamouri A.;
"Guanine glycation repair by DJ-1/Park7 and its bacterial homologs.";
Science 357:208-211(2017).
[9]
X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS) OF 2-172.
PubMed=14649299; DOI=10.1023/A:1026177202925;
Abergel C., Coutard B., Byrne D., Chenivesse S., Claude J.-B.,
Deregnaucourt C., Fricaux T., Gianesini-Boutreux C., Jeudy S.,
Lebrun R., Maza C., Notredame C., Poirot O., Suhre K., Varagnol M.,
Claverie J.-M.;
"Structural genomics of highly conserved microbial genes of unknown
function in search of new antibacterial targets.";
J. Struct. Funct. Genomics 4:141-157(2003).
-!- FUNCTION: Protein and nucleotide deglycase that catalyzes the
deglycation of the Maillard adducts formed between amino groups of
proteins or nucleotides and reactive carbonyl groups of glyoxals
(PubMed:26774339, PubMed:28596309). Thus, functions as a protein
deglycase that repairs methylglyoxal- and glyoxal-glycated
proteins, and releases repaired proteins and lactate or glycolate,
respectively. Deglycates cysteine, arginine and lysine residues in
proteins, and thus reactivates these proteins by reversing
glycation by glyoxals. Is able to repair glycated serum albumin,
collagen, glyceraldehyde-3-phosphate dehydrogenase, and fructose
biphosphate aldolase. Acts on early glycation intermediates
(hemithioacetals and aminocarbinols), preventing the formation of
advanced glycation endproducts (AGE) that cause irreversible
damage (PubMed:26774339). Also functions as a nucleotide deglycase
able to repair glycated guanine in the free nucleotide pool (GTP,
GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major
nucleotide repair system named guanine glycation repair (GG
repair), dedicated to reversing methylglyoxal and glyoxal damage
via nucleotide sanitization and direct nucleic acid repair
(PubMed:28596309). In vitro, prevents acrylamide formation in
asparagine/glyoxal and asparagine/sugar mixtures at 55 degrees
Celsius, likely by degrading asparagine/glyoxal Maillard adducts
formed at high temperatures (PubMed:27530919). Also displays an
apparent glyoxalase activity that in fact reflects its deglycase
activity (PubMed:26774339, PubMed:26678554). Is a general stress
protein; is required for the protection of bacterial cells against
many environmental stresses, including oxidative, thermal,
osmotic, UV, and pH stresses (PubMed:17933887). And plays an
important role in protection against electrophile/carbonyl stress
(PubMed:26774339). {ECO:0000269|PubMed:17933887,
ECO:0000269|PubMed:26678554, ECO:0000269|PubMed:26774339,
ECO:0000269|PubMed:27530919, ECO:0000269|PubMed:28596309}.
-!- CATALYTIC ACTIVITY: An N(omega)-(1-hydroxy-2-oxopropyl)-[protein]-
L-arginine + H(2)O = a [protein]-L-arginine + (R)-lactate.
{ECO:0000305|PubMed:26774339}.
-!- CATALYTIC ACTIVITY: An N(6)-(1-hydroxy-2-oxopropyl)-[protein]-L-
lysine + H(2)O = a [protein]-L-lysine + (R)-lactate.
{ECO:0000305|PubMed:26774339}.
-!- CATALYTIC ACTIVITY: An S-(1-hydroxy-2-oxopropyl)-[protein]-L-
cysteine + H(2)O = a [protein]-L-cysteine + (R)-lactate.
{ECO:0000305|PubMed:26774339}.
-!- ENZYME REGULATION: Glyoxalase activity is inhibited by zinc ions
at pH 7.0. {ECO:0000269|PubMed:26678554}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.38 mM for glyoxal (at pH 7.4 and 37 degrees Celsius)
{ECO:0000269|PubMed:26678554};
KM=0.06 mM for methylglyoxal (at pH 7.4 and 37 degrees Celsius)
{ECO:0000269|PubMed:26678554};
Note=kcat is 118.44 min(-1) and 20.80 min (-1) for glyoxalase
activity with glyoxal (GO) and methylglyoxal (MGO) as substrate,
respectively (at pH 7.4 and 37 degrees Celsius)
(PubMed:26678554). The apparent kcat of MGO and GO degradation
is 0.29 sec(-1), and 0.42 sec(-1), respectively (at 22 degrees
Celsius) (PubMed:26774339). {ECO:0000269|PubMed:26678554,
ECO:0000269|PubMed:26774339};
-!- SUBUNIT: Exists in monomeric, trimeric, and hexameric forms.
{ECO:0000269|PubMed:16380269}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:16380269}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene are highly sensitive
to oxidative, thermal, UV, and pH stresses, but only slightly
sensitive to salt stress and insensitive to cold stress
(PubMed:17933887). They display increased protein glycation
levels, and decreased viability in methylglyoxal- or glucose-
containing media (PubMed:26774339). They also show highly
increased DNA and RNA glycation levels, and exhibit strong mutator
phenotypes (PubMed:28596309). Moreover, the double and triple
mutants lacking yhbO and yajL, and yhbO, yajL and hchA,
respectively, display impressive amounts of glycated proteins,
suggesting that the YhbO, YajL and Hsp31 deglycases display
relatively redundant functions (PubMed:26774339). The triple
mutant displays higher glycation levels of free nucleotides (GTP
and dGTP) than the parental strain, and shows higher glycation
levels of DNA and RNA than those of single mutants
(PubMed:28596309). {ECO:0000269|PubMed:17933887,
ECO:0000269|PubMed:26774339}.
-!- SIMILARITY: Belongs to the peptidase C56 family. {ECO:0000305}.
-!- CAUTION: The protein deglycation activity has been ascribed to a
TRIS buffer artifact by a publication (PubMed:27903648), which has
then been rebutted by clear biochemical experiments showing that
DJ-1 family deglycases are bona fide deglycases (PubMed:28013050).
Deglycase activity is even strengthened by a novel article that
reports nucleotide deglycation activity (PubMed:28596309).
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAA57956.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; U18997; AAA57956.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC76187.2; -; Genomic_DNA.
EMBL; AP009048; BAE77199.1; -; Genomic_DNA.
RefSeq; NP_417622.2; NC_000913.3.
RefSeq; WP_000037608.1; NZ_LN832404.1.
PDB; 1OI4; X-ray; 2.03 A; A/B=2-172.
PDBsum; 1OI4; -.
ProteinModelPortal; P45470; -.
SMR; P45470; -.
BioGrid; 4259270; 10.
DIP; DIP-12263N; -.
STRING; 316385.ECDH10B_3326; -.
MEROPS; C56.976; -.
PaxDb; P45470; -.
PRIDE; P45470; -.
EnsemblBacteria; AAC76187; AAC76187; b3153.
EnsemblBacteria; BAE77199; BAE77199; BAE77199.
GeneID; 947666; -.
KEGG; ecj:JW5529; -.
KEGG; eco:b3153; -.
PATRIC; fig|1411691.4.peg.3577; -.
EchoBASE; EB2637; -.
EcoGene; EG12784; yhbO.
eggNOG; ENOG4107R7Y; Bacteria.
eggNOG; COG0693; LUCA.
HOGENOM; HOG000063195; -.
InParanoid; P45470; -.
KO; K05520; -.
OMA; MVGHTVH; -.
PhylomeDB; P45470; -.
BioCyc; EcoCyc:G7647-MONOMER; -.
BioCyc; MetaCyc:G7647-MONOMER; -.
EvolutionaryTrace; P45470; -.
PRO; PR:P45470; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0019172; F:glyoxalase III activity; IDA:EcoCyc.
GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
GO; GO:0036524; F:protein deglycase activity; IDA:EcoCyc.
GO; GO:0006281; P:DNA repair; IMP:EcoCyc.
GO; GO:0006517; P:protein deglycosylation; IDA:EcoCyc.
GO; GO:0030091; P:protein repair; IDA:EcoCyc.
GO; GO:0009408; P:response to heat; IMP:EcoCyc.
GO; GO:0006979; P:response to oxidative stress; IMP:EcoCyc.
GO; GO:0009268; P:response to pH; IMP:EcoCyc.
GO; GO:0009411; P:response to UV; IMP:EcoCyc.
Gene3D; 3.40.50.880; -; 1.
InterPro; IPR006286; C56_PfpI.
InterPro; IPR029062; Class_I_gatase-like.
InterPro; IPR002818; DJ-1/PfpI.
Pfam; PF01965; DJ-1_PfpI; 1.
SUPFAM; SSF52317; SSF52317; 1.
TIGRFAMs; TIGR01382; PfpI; 1.
PROSITE; PS51276; PEPTIDASE_C56_PFPI; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
DNA damage; DNA repair; Hydrolase; Reference proteome;
Stress response.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:16380269}.
CHAIN 2 172 Protein/nucleic acid deglycase 2.
/FTId=PRO_0000157831.
DOMAIN 3 171 PfpI endopeptidase. {ECO:0000255|PROSITE-
ProRule:PRU00608}.
ACT_SITE 104 104 Nucleophile.
{ECO:0000250|UniProtKB:P31658}.
MUTAGEN 104 104 C->A: Unable to complement the gene
deletion mutant, in contrast to the wild-
type allele that rescues the oxidative-
stress and thermal-stress sensitive
phenotypes.
{ECO:0000269|PubMed:17933887}.
STRAND 4 8 {ECO:0000244|PDB:1OI4}.
HELIX 16 27 {ECO:0000244|PDB:1OI4}.
STRAND 31 38 {ECO:0000244|PDB:1OI4}.
STRAND 42 44 {ECO:0000244|PDB:1OI4}.
STRAND 51 53 {ECO:0000244|PDB:1OI4}.
HELIX 58 60 {ECO:0000244|PDB:1OI4}.
HELIX 63 65 {ECO:0000244|PDB:1OI4}.
STRAND 67 71 {ECO:0000244|PDB:1OI4}.
HELIX 76 80 {ECO:0000244|PDB:1OI4}.
HELIX 84 95 {ECO:0000244|PDB:1OI4}.
STRAND 100 103 {ECO:0000244|PDB:1OI4}.
TURN 104 106 {ECO:0000244|PDB:1OI4}.
HELIX 107 113 {ECO:0000244|PDB:1OI4}.
HELIX 125 127 {ECO:0000244|PDB:1OI4}.
HELIX 128 133 {ECO:0000244|PDB:1OI4}.
STRAND 144 146 {ECO:0000244|PDB:1OI4}.
TURN 147 149 {ECO:0000244|PDB:1OI4}.
STRAND 150 155 {ECO:0000244|PDB:1OI4}.
HELIX 156 158 {ECO:0000244|PDB:1OI4}.
HELIX 159 170 {ECO:0000244|PDB:1OI4}.
SEQUENCE 172 AA; 18858 MW; CF9E2E405788125E CRC64;
MSKKIAVLIT DEFEDSEFTS PADEFRKAGH EVITIEKQAG KTVKGKKGEA SVTIDKSIDE
VTPAEFDALL LPGGHSPDYL RGDNRFVTFT RDFVNSGKPV FAICHGPQLL ISADVIRGRK
LTAVKPIIID VKNAGAEFYD QEVVVDKDQL VTSRTPDDLP AFNREALRLL GA


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