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Protein

Protein 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 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) (PubMed:26774339). 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).3 Publications

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

Manual assertion based on experiment ini

  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: GO_Central
    • hydrolase activity Source: UniProtKB-KW
    • identical protein binding Source: EcoCyc

    GO - Biological processi

    • methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione Source: GO_Central
    • response to heat Source: EcoCyc
    • response to oxidative stress Source: EcoCyc
    • response to pH Source: EcoCyc
    • response to UV Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Stress response

    Enzyme and pathway databases

    BioCyciEcoCyc:G7647-MONOMER.
    ECOL316407:JW5529-MONOMER.
    MetaCyc:G7647-MONOMER.

    Protein family/group databases

    MEROPSiC56.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein deglycase 21 Publication (EC:3.1.2.-1 Publication, EC:3.5.1.-1 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

    Complete GO annotation...

    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 glycation levels, and decreased viability in methylglyoxal- or glucose-containing media (PubMed:26774339). 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).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 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.
    STRINGi511145.b3153.

    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
    Contains 1 PfpI endopeptidase domain.PROSITE-ProRule annotation

    Phylogenomic databases

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

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002818. DJ-1/PfpI.
    IPR006286. Peptidase_C56.
    [Graphical view]
    PfamiPF01965. DJ-1_PfpI. 1 hit.
    [Graphical view]
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR01382. PfpI. 1 hit.
    PROSITEiPS51276. PEPTIDASE_C56_PFPI. 1 hit.
    [Graphical view]

    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.
    PATRICi32121724. VBIEscCol129921_3248.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    DIPiDIP-12263N.
    STRINGi511145.b3153.

    Protein family/group databases

    MEROPSiC56.001.

    Proteomic databases

    PaxDbiP45470.
    PRIDEiP45470.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76187; AAC76187; b3153.
    BAE77199; BAE77199; BAE77199.
    GeneIDi947666.
    KEGGiecj:JW5529.
    eco:b3153.
    PATRICi32121724. VBIEscCol129921_3248.

    Organism-specific databases

    EchoBASEiEB2637.
    EcoGeneiEG12784. yhbO.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyciEcoCyc:G7647-MONOMER.
    ECOL316407:JW5529-MONOMER.
    MetaCyc:G7647-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP45470.
    PROiP45470.

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002818. DJ-1/PfpI.
    IPR006286. Peptidase_C56.
    [Graphical view]
    PfamiPF01965. DJ-1_PfpI. 1 hit.
    [Graphical view]
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR01382. PfpI. 1 hit.
    PROSITEiPS51276. PEPTIDASE_C56_PFPI. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYHBO_ECOLI
    AccessioniPrimary (citable) accession number: P45470
    Secondary accession number(s): Q2M957
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: May 30, 2000
    Last modified: November 2, 2016
    This is version 125 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.