C5G6D7 · CABC2_BACT4

Function

function

Broad-specificity glycosaminoglycan lyase, which acts in an exolytic fashion degrading chondroitin sulfates and dermatan sulfate to yield only disaccharide products. Has a preference for chondroitin 4-sulfate over chondroitin 6-sulfate. Has extremely low activity against hyaluronic acid. Is not active against acharan sulfate, heparin or heparan sulfate.

Catalytic activity

  • Exolytic removal of Delta4-unsaturated disaccharide residues from the non-reducing ends of both polymeric chondroitin/dermatan sulfates and their oligosaccharide fragments.
    EC:4.2.2.21 (UniProtKB | ENZYME | Rhea)

Cofactor

Ca2+ (UniProtKB | Rhea| CHEBI:29108 )

Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: Divalent metal cation. Requires divalent metal cation for binding of dermatan sulfate substrate, whereas it is not necessary for the binding of chondroitin sulfate substrates. Prefers Ca2+ or Mg2+, binding 1 ion per subunit.

Activity regulation

Specific activity for chondroitin sulfate substrates increases moderately (2-fold) while an increase of 25-fold is observed for dermatan sulfate as substrate upon addition of Ca2+ or Mg2+ ions (PubMed:18227125).
Increasing the concentration of Na+, K+ or Cs+ chloride from 0 to 0.1 M, increases the activity against all substrates. Further increases in salt concentration reduces the activity dramatically, with 50% inhibition occurring at 0.15 M and nearly complete inhibition at 0.4 M salt. The addition of 10 mM Ca2+ or Mg2+ ions increases the activity against chondroitin 4- and 6-sulfates by 2-3-fold, while the activity against dermatan sulfate increases much more significantly by 50-fold (PubMed:18512954).
Addition of Mn2+ and Zn2+ reduces activity against chondroitin sulfate substrates, but increases the activity against dermatan sulfate. Increasing the concentration of CaCl2 with both chondroitin 4- and 6-sulfates from 0 to 0.04 M increases the activity. A further increase reduces activity, with 50% inhibition at 0.065-0.085 M and a complete inhibition of the reaction at 0.2 M. In case of dermatan sulfate, the addition of low concentration of CaCl2 dramatically increases the activity from the basal level. The maximal activity is reached at 0.01 M CaCl2.

Kinetics

KM SUBSTRATE pH TEMPERATURE[C] NOTES EVIDENCE
67 μMchondroitin 4-sulfate from porcine or bovine trachea7.637
33 μMchondroitin 6-sulfate from shark cartilage7.637
61 μMdermatan sulfate from porcine intestinal mucosa7.637
Vmax pH TEMPERATURE[C] NOTES EVIDENCE
77.6 μmol/min/mg7.637with chondroitin 4-sulfate from bovine trachea as substrate, in 50 mM phosphate
47.4 μmol/min/mg7.637with chondroitin 6-sulfate from shark cartilage as substrate, in 50 mM phosphate
14.4 μmol/min/mg7.637with chondroitin 2,6-sulfate from skate cartilage as substrate, in 50 mM phosphate
28.5 μmol/min/mg7.637with chondroitin 4,6-sulfate from squid cartilage as substrate, in 50 mM phosphate
9.1 μmol/min/mg7.637with dermatan sulfate from porcine intestinal mucosa as substrate, in 50 mM phosphate
kcat is 15792 min-1 with chondroitin 4-sulfate from porcine or bovine trachea as substrate. kcat is 10404 min-1 with chondroitin 6-sulfate from shark cartilage as substrate. kcat is 2307 min-1 with dermatan sulfate from porcine intestinal mucosa as substrate.

pH Dependence

Optimum pH is 7.6. Decreased activity at pH values below 7.0 and above 8.0. The activity against chondroitin 6-sulfate remains higher than with other substrates at low pH. At pH 6.5 the enzyme exhibits almost 60% of its maximal activity against chondroitin 6-sulfate, only 20% activity against chondroitin 4-sulfate and no measurable activity against dermatan sulfate. In contrast, at pH of 8.5 about 30% of enzyme's maximal activity against all substrates is displayed.

Temperature Dependence

Optimum temperature is 37 degrees Celsius. No significant reduction in activity at temperatures in the range of 25-40 degrees Celsius. At 50 degrees Celsius, activity of 45% for dermatan sulfate, 60% for chondroitin 4-sulfate and 75% for chondroitin 6-sulfate is detected. Thermal denaturation curve is bimodal with two consecutive thermal denaturation midpoints (Tm) corresponding to 44 and 50 degrees Celsius, respectively.

Features

Showing features for binding site, site, active site.

TypeIDPosition(s)Description
Binding site24Ca2+ (UniProtKB | ChEBI)
Binding site26Ca2+ (UniProtKB | ChEBI)
Binding site50Ca2+ (UniProtKB | ChEBI)
Binding site53Ca2+ (UniProtKB | ChEBI)
Binding site161Ca2+ (UniProtKB | ChEBI)
Site172Important for catalytic activity against all substrates
Site344Important for catalytic activity against dermatan sulfate substrate
Active site345Proton acceptor
Active site454Proton acceptor
Active site461Proton donor
Site514Transition state stabilizer
Site628Important for catalytic activity against all substrates

GO annotations

AspectTerm
Cellular Componentextracellular region
Cellular Componentperiplasmic space
Molecular Functioncalcium ion binding
Molecular Functioncarbohydrate binding
Molecular Functionchondroitin-sulfate-ABC endolyase activity
Molecular Functionchondroitin-sulfate-ABC exolyase activity
Molecular Functionmagnesium ion binding
Biological Processcarbohydrate metabolic process
Biological Processdermatan sulfate catabolic process
Biological Processglycosaminoglycan catabolic process

Keywords

Enzyme and pathway databases

Protein family/group databases

    • PL8Polysaccharide Lyase Family 8

Names & Taxonomy

Protein names

  • Recommended name
    Chondroitin sulfate ABC exolyase
  • EC number
  • Alternative names
    • Chondroitin ABC exoeliminase
    • Chondroitin ABC lyase II
    • Chondroitin sulfate ABC lyase II
      (ChS ABC lyase II
      )
    • Chondroitinase ABC II
      (cABC II
      )
    • Exochondroitinase ABC

Gene names

    • Name
      chonabc

Organism names

  • Taxonomic identifier
  • Strain
    • ATCC 29741 / DSM 2255 / WAL 2926
  • Taxonomic lineage
    Bacteria > Bacteroidota > Bacteroidia > Bacteroidales > Bacteroidaceae > Bacteroides

Accessions

  • Primary accession
    C5G6D7

Subcellular Location

Keywords

Phenotypes & Variants

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis172Loss of activity against all substrates.
Mutagenesis173Reduced activity against all substrates by a factor of about 2-10.
Mutagenesis267Reduced activity against all substrates by a factor of about 2-10.
Mutagenesis344No detectable activity against dermatan sulfate in the standard assay, but after overnight incubation shows traces of degradation products, also still degrades chondroitin sulfate albeit with 10- to 30-fold lower catalytic efficiency.
Mutagenesis344Loss of activity against all substrates.
Mutagenesis344Retains 5-25% catalytic efficiency against all substrates.
Mutagenesis344Retains 5% catalytic efficiency against chondroitin 4-sulfate only.
Mutagenesis345No activity against dermatan sulfate even after overnight incubation, but still degrades chondroitin sulfate albeit with 10- to 30-fold lower catalytic efficiency.
Mutagenesis345Loss of activity against all substrates.
Mutagenesis345Low levels of activity against chondroitin sulfate substrates, but no activity against dermatan sulfate.
Mutagenesis453Slightly reduced activity against all substrates.
Mutagenesis453Shows no activity against dermatan sulfate while retaining about 10% of its catalytic efficiency against chondroitin 4- and 6-sulfates.
Mutagenesis454Loss of activity against all substrates.
Mutagenesis461Loss of activity against all substrates.
Mutagenesis514Loss of activity against all substrates.
Mutagenesis628Loss of activity against all substrates.
Mutagenesis628Retains low levels of activity against chondroitin sulfate substrates, but not against dermatan sulfate as substrate.

PTM/Processing

Features

Showing features for signal, chain.

TypeIDPosition(s)Description
Signal1-14
ChainPRO_000042012315-1014Chondroitin sulfate ABC exolyase

Interaction

Subunit

Monomer.

Family & Domains

Sequence similarities

Belongs to the polysaccharide lyase 8 family.

Keywords

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Sequence processing
    The displayed sequence is further processed into a mature form.
  • Length
    1,014
  • Mass (Da)
    114,921
  • Last updated
    2012-10-31 v2
  • Checksum
    10C46B91CF02A44A
MLILSFLCPAFLNAQIVTDERMFSFEEPQLPACITGVQSQLGISGAHYKDGKHSLEWTFEPNGRLELRKDLKFEKKDPTGKDLYLSAFIVWIYNEQPQDAAIEFEFLKDGRKCASFPFGINFKGWRAAWVCYERDMQGTPEEGMNELRIVAPDAKGRLFIDHLITATKVDARQQTADLQVPFVNAGTTNHWLVLYKHSLLKPDIELTPVSDKQRQEMKLLEKRFRDMIYTKGKVTEKEAETIRKKYDLYQITYKDGQVSGVPVFMVRASEAYERMIPDWDKDMLTKMGIEMRAYFDLMKRIAVAYNNSEAGSPIRKEMRRKFLAMYDHITDQGVAYGSCWGNIHHYGYSVRGLYPAYFLMKDVLREEGKLLEAERTLRWYAITNEVYPKPEGNGIDMDSFNTQTTGRIASILMMEDTPEKLQYLKSFSRWIDYGCRPAPGLAGSFKVDGGAFHHRNNYPAYAVGGLDGATNMIYLFSRTSLAVSELAHRTVKDVLLAMRFYCNKLNFPLSMSGRHPDGKGKLVPMHYAIMAIAGTPDGKGDFDKEMASAYLRLVSSDSSSAEQAPEYMPKVSNAQERKIAKRLVENGFRAEPDPQGNLSLGYGCVSVQRRENWSAVARGHSRYLWAAEHYLGHNLYGRYLAHGSLQILTAPPGQTVTPTTSGWQQEGFDWNRIPGVTSIHLPLDLLKANVLNVDTFSGMEEMLYSDEAFAGGLSQGKMNGNFGMKLHEHDKYNGTHRARKSFHFIDGMIVCLGSDIENTNMDYPTETTIFQLAVTDKAAHDYWKNNAGEGKVWMDHLGTGYYVPVAARFEKNFPQYSRMQDTGKETKGDWVSLIIDHGKAPKAGSYEYAILPGTDRKTMTAFAKKPAYSVLQQDRNAHILESPSDRITSYVLFETPQSLLPGGLLQRTDTSCLVMVRKESADKVLLTVAQPDLALYRGPSDEAFDKDGKRMERSIYSRPWIDNESGEIPVTVTLKGRWKVVETPYCKVVSEDKKQTVLRFLCKDGASYEVELEK

Sequence caution

The sequence ABV21364.1 differs from that shown. Reason: Miscellaneous discrepancy Cloning artifact.

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
EF639172
EMBL· GenBank· DDBJ
ABV21364.1
EMBL· GenBank· DDBJ
Genomic DNA Sequence problems.

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