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Protein

Protein/nucleic acid deglycase 3

Gene

yajL

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 Schiff bases and advanced glycation endproducts (AGE) that cause irreversible damage (PubMed:25416785, 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. However, is less efficient than Hsp31 and YhbO, suggesting that YajL might be preferentially dedicated to protein repair (PubMed:28596309). Displays a covalent chaperone activity with sulfenylated thiol proteins by forming mixed disulfides with members of the thiol proteome, and preferentially with sulfenylated cellular proteins, upon oxidative stress; these mixed disulfides can be subsequently reduced by low-molecular-weight thiols to regenerate YajL and reduced proteins (PubMed:22157000, PubMed:22321799). Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone (PubMed:20889753). Confers resistance to oxidative stress (PubMed:20124404, PubMed:22157000, PubMed:22321799). Plays an important role in protection against electrophile/carbonyl stress (PubMed:26774339). The chaperone activity reported for YajL is probably recruited to execute its deglycase activity, to interact with non-native glycated proteins and gain access to partially buried glycated sites (PubMed:25416785, PubMed:26774339). Also displays an apparent glyoxalase activity that in fact reflects its deglycase activity (PubMed:26774339, PubMed:26678554).8 Publications

Catalytic activityi

An N(omega)-(1-hydroxy-2-oxopropyl)-[protein]-L-arginine + H2O = a [protein]-L-arginine + (R)-lactate.1 Publication
An N6-(1-hydroxy-2-oxopropyl)-[protein]-L-lysine + H2O = a [protein]-L-lysine + (R)-lactate.1 Publication
An S-(1-hydroxy-2-oxopropyl)-[protein]-L-cysteine + H2O = a [protein]-L-cysteine + (R)-lactate.1 Publication

Enzyme regulationi

Glyoxalase activity is inhibited by zinc ions (PubMed:26678554). Active as a chaperone in both its reduced and oxidized states, and is more active in its oxidized form (PubMed:20124404).2 Publications

Kineticsi

kcat is 70.32 min(-1) for glyoxalase activity with glyoxal as substrate (at pH 7.4 and 37 degrees Celsius) (PubMed:26678554). The apparent kcat of methylglyoxal and glyoxal degradation is 0.08 sec(-1), and 0.15 sec(-1), respectively (at 22 degrees Celsius) (PubMed:26774339).2 Publications
  1. KM=2.97 mM for glyoxal (at pH 7.4 and 37 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei106NucleophileCurated1

    GO - Molecular functioni

    • hydrolase activity Source: UniProtKB-KW
    • protein deglycase activity Source: EcoCyc

    GO - Biological processi

    • cellular response to oxidative stress Source: UniProtKB
    • protein deglycosylation Source: EcoCyc
    • protein refolding Source: EcoCyc
    • protein repair Source: EcoCyc
    • response to heat Source: EcoCyc
    • ribosome biogenesis Source: UniProtKB

    Keywordsi

    Molecular functionChaperone, Hydrolase
    Biological processDNA damage, DNA repair, Stress response

    Enzyme and pathway databases

    BioCyciEcoCyc:HMP-KIN-MONOMER.
    MetaCyc:HMP-KIN-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein/nucleic acid deglycase 32 Publications (EC:3.1.2.-1 Publication, EC:3.5.1.-1 Publication, EC:3.5.1.1241 Publication)
    Alternative name(s):
    Chaperone protein YajL
    Maillard deglycase1 Publication
    Gene namesi
    Name:yajL
    Synonyms:thiJ
    Ordered Locus Names:b0424, JW5057
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13272. yajL.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene display highest sensitivity to carbonyl stress. The yajL mutant (but not the parental strain) suffers from a 100-fold decrease in viability after incubation for 48 h in LB medium containing 0.6% glucose, and the mutant is rescued by YajL- and DJ-1-overproducing plasmids. The wild-type strain displays a small quantity of glycated proteins after overnight culture in LB medium supplemented with 0.6% glucose, whereas the yajL mutant displays much higher levels of glycated proteins (PubMed:25416785, PubMed:26774339), and also higher DNA and RNA glycation levels (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). The yajL mutant cells display decreased viability in methylglyoxal- or glucose-containing media (PubMed:26774339). They also display increased protein sulfenic acids levels, both before and after oxidative stress, but similar protein disulfides levels (PubMed:22321799). In aerobiosis, mutants show a protein aggregation phenotype, which is increased by oxidative stress (PubMed:20124404). Mutants show also altered gene expression and display decreased translation accuracy (PubMed:20889753). The yajL deletion mutant shows a negligible NADH dehydrogenase 1 activity and compensates for this low activity by utilizing NADH-independent alternative dehydrogenases, including pyruvate oxidase PoxB and D-aminoacid dehydrogenase DadA, and mixed acid aerobic fermentations characterized by acetate, lactate, succinate and ethanol excretion (PubMed:26377309). It shows up-regulation of genes involved in glycolytic and pentose phosphate pathways and alternative respiratory pathways (PubMed:26377309). Moreover, the yajL mutant preferentially catabolizes pyruvate-forming amino acids over Krebs cycle-related ones, and thus it utilizes pyruvate-centred respiro-fermentative metabolism to compensate for the NADH dehydrogenase 1 defect (PubMed:26377309).7 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi47C → A: Is not impaired in the formation of mixed disulfide with a sulfenylated protein. Has a monomeric quaternary structure. 2 Publications1
    Mutagenesisi106C → A: Is impaired in the formation of mixed disulfide with cytoplasmic and sulfenylated proteins. Does not complement a disruption mutant. 3 Publications1
    Mutagenesisi106C → D: Does not complement a disruption mutant. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001578291 – 196Protein/nucleic acid deglycase 3Add BLAST196

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei106Cysteine sulfinic acid (-SO2H); alternate1 Publication1

    Post-translational modificationi

    Cys-106 is easily oxidized to sulfinic acid.1 Publication

    Keywords - PTMi

    Oxidation

    Proteomic databases

    PaxDbiQ46948.
    PRIDEiQ46948.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    BioGridi4263345. 4 interactors.
    849455. 57 interactors.
    IntActiQ46948. 17 interactors.
    STRINGi316385.ECDH10B_0380.

    Structurei

    Secondary structure

    1196
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 9Combined sources6
    Helixi15 – 27Combined sources13
    Beta strandi31 – 36Combined sources6
    Beta strandi44 – 46Combined sources3
    Beta strandi52 – 54Combined sources3
    Beta strandi56 – 58Combined sources3
    Helixi59 – 62Combined sources4
    Beta strandi68 – 72Combined sources5
    Helixi76 – 84Combined sources9
    Helixi86 – 97Combined sources12
    Beta strandi101 – 105Combined sources5
    Helixi108 – 112Combined sources5
    Turni113 – 117Combined sources5
    Beta strandi118 – 122Combined sources5
    Helixi128 – 133Combined sources6
    Turni136 – 138Combined sources3
    Beta strandi143 – 147Combined sources5
    Turni148 – 151Combined sources4
    Beta strandi152 – 155Combined sources4
    Helixi158 – 160Combined sources3
    Helixi161 – 172Combined sources12
    Helixi175 – 182Combined sources8
    Turni183 – 186Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2AB0X-ray1.10A/B1-196[»]
    5SY4X-ray0.98A/B1-196[»]
    ProteinModelPortaliQ46948.
    SMRiQ46948.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ46948.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase C56 family.Curated

    Phylogenomic databases

    eggNOGiENOG4107S0N. Bacteria.
    COG0693. LUCA.
    HOGENOMiHOG000063194.
    InParanoidiQ46948.
    KOiK03152.
    PhylomeDBiQ46948.

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    InterProiView protein in InterPro
    IPR029062. Class_I_gatase-like.
    IPR002818. DJ-1/PfpI.
    IPR006287. DJ1.
    PfamiView protein in Pfam
    PF01965. DJ-1_PfpI. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR01383. not_thiJ. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q46948-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSASALVCLA PGSEETEAVT TIDLLVRGGI KVTTASVASD GNLAITCSRG
    60 70 80 90 100
    VKLLADAPLV EVADGEYDVI VLPGGIKGAE CFRDSTLLVE TVKQFHRSGR
    110 120 130 140 150
    IVAAICAAPA TVLVPHDIFP IGNMTGFPTL KDKIPAEQWL DKRVVWDARV
    160 170 180 190
    KLLTSQGPGT AIDFGLKIID LLVGREKAHE VASQLVMAAG IYNYYE
    Length:196
    Mass (Da):20,777
    Last modified:May 30, 2000 - v2
    Checksum:i15282395CCF2CE75
    GO

    Sequence cautioni

    The sequence AAA82704 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence AAB40180 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U34923 Genomic DNA. Translation: AAA82704.1. Different initiation.
    U82664 Genomic DNA. Translation: AAB40180.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73527.2.
    AP009048 Genomic DNA. Translation: BAE76204.1.
    PIRiH64771.
    RefSeqiNP_414958.4. NC_000913.3.
    WP_001276305.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73527; AAC73527; b0424.
    BAE76204; BAE76204; BAE76204.
    GeneIDi945066.
    KEGGiecj:JW5057.
    eco:b0424.
    PATRICifig|1411691.4.peg.1853.

    Similar proteinsi

    Entry informationi

    Entry nameiYAJL_ECOLI
    AccessioniPrimary (citable) accession number: Q46948
    Secondary accession number(s): Q2MC02
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: May 30, 2000
    Last modified: September 27, 2017
    This is version 133 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally (Ref. 1) thought to be involved in thiamine biosynthesis. However, this phenotype was probably due to an artifactual recombination event involving a portion of the adjacent thiI gene.Curated
    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).Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Peptidase families
      Classification of peptidase families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families