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Protein

Protein/nucleic acid deglycase 2

Gene

yhbO

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 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).5 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 at pH 7.0.1 Publication

Kineticsi

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).2 Publications
  1. KM=0.38 mM for glyoxal (at pH 7.4 and 37 degrees Celsius)1 Publication
  2. KM=0.06 mM for methylglyoxal (at pH 7.4 and 37 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei104NucleophileBy similarity1

    GO - Molecular functioni

    • glyoxalase III activity Source: EcoCyc
    • hydrolase activity Source: UniProtKB-KW
    • identical protein binding Source: EcoCyc
    • protein deglycase activity Source: EcoCyc

    GO - Biological processi

    • DNA repair Source: UniProtKB-KW
    • protein deglycosylation Source: EcoCyc
    • protein repair Source: EcoCyc
    • response to heat Source: EcoCyc
    • response to oxidative stress Source: EcoCyc
    • response to pH Source: EcoCyc
    • response to UV Source: EcoCyc

    Keywordsi

    Molecular functionHydrolase
    Biological processDNA damage, DNA repair, Stress response

    Enzyme and pathway databases

    BioCyciEcoCyc:G7647-MONOMER.
    MetaCyc:G7647-MONOMER.

    Protein family/group databases

    MEROPSiC56.976.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein/nucleic acid deglycase 22 Publications (EC:3.1.2.-1 Publication, EC:3.5.1.-1 Publication, EC:3.5.1.1241 Publication)
    Alternative name(s):
    Maillard deglycase1 Publication
    Gene namesi
    Name:yhbO
    Ordered Locus Names:b3153, JW5529
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12784. yhbO.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    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).2 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi104C → 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. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001578312 – 172Protein/nucleic acid deglycase 2Add BLAST171

    Proteomic databases

    PaxDbiP45470.
    PRIDEiP45470.

    Interactioni

    Subunit structurei

    Exists in monomeric, trimeric, and hexameric forms.1 Publication

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    DIPiDIP-12263N.
    STRINGi316385.ECDH10B_3326.

    Structurei

    Secondary structure

    1172
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 8Combined sources5
    Helixi16 – 27Combined sources12
    Beta strandi31 – 38Combined sources8
    Beta strandi42 – 44Combined sources3
    Beta strandi51 – 53Combined sources3
    Helixi58 – 60Combined sources3
    Helixi63 – 65Combined sources3
    Beta strandi67 – 71Combined sources5
    Helixi76 – 80Combined sources5
    Helixi84 – 95Combined sources12
    Beta strandi100 – 103Combined sources4
    Turni104 – 106Combined sources3
    Helixi107 – 113Combined sources7
    Helixi125 – 127Combined sources3
    Helixi128 – 133Combined sources6
    Beta strandi144 – 146Combined sources3
    Turni147 – 149Combined sources3
    Beta strandi150 – 155Combined sources6
    Helixi156 – 158Combined sources3
    Helixi159 – 170Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1OI4X-ray2.03A/B2-172[»]
    ProteinModelPortaliP45470.
    SMRiP45470.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45470.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini3 – 171PfpI endopeptidasePROSITE-ProRule annotationAdd BLAST169

    Sequence similaritiesi

    Belongs to the peptidase C56 family.Curated

    Phylogenomic databases

    eggNOGiENOG4107R7Y. Bacteria.
    COG0693. LUCA.
    HOGENOMiHOG000063195.
    InParanoidiP45470.
    KOiK05520.
    PhylomeDBiP45470.

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    InterProiView protein in InterPro
    IPR006286. C56_PfpI.
    IPR029062. Class_I_gatase-like.
    IPR002818. DJ-1/PfpI.
    PfamiView protein in Pfam
    PF01965. DJ-1_PfpI. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR01382. PfpI. 1 hit.
    PROSITEiView protein in PROSITE
    PS51276. PEPTIDASE_C56_PFPI. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P45470-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKKIAVLIT DEFEDSEFTS PADEFRKAGH EVITIEKQAG KTVKGKKGEA
    60 70 80 90 100
    SVTIDKSIDE VTPAEFDALL LPGGHSPDYL RGDNRFVTFT RDFVNSGKPV
    110 120 130 140 150
    FAICHGPQLL ISADVIRGRK LTAVKPIIID VKNAGAEFYD QEVVVDKDQL
    160 170
    VTSRTPDDLP AFNREALRLL GA
    Length:172
    Mass (Da):18,858
    Last modified:May 30, 2000 - v2
    Checksum:iCF9E2E405788125E
    GO

    Sequence cautioni

    The sequence AAA57956 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA57956.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76187.2.
    AP009048 Genomic DNA. Translation: BAE77199.1.
    RefSeqiNP_417622.2. NC_000913.3.
    WP_000037608.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76187; AAC76187; b3153.
    BAE77199; BAE77199; BAE77199.
    GeneIDi947666.
    KEGGiecj:JW5529.
    eco:b3153.
    PATRICifig|1411691.4.peg.3577.

    Similar proteinsi

    Entry informationi

    Entry nameiYHBO_ECOLI
    AccessioniPrimary (citable) accession number: P45470
    Secondary accession number(s): Q2M957
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: May 30, 2000
    Last modified: November 22, 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

    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, Direct protein sequencing, 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