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Protein

Chondroitin sulfate ABC exolyase

Gene

chonabc

Organism
Bacteroides thetaiotaomicron
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

Exolytic removal of Delta(4)-unsaturated disaccharide residues from the non-reducing ends of both polymeric chondroitin/dermatan sulfates and their oligosaccharide fragments.2 Publications

Cofactori

Ca2+2 Publications, Mg2+2 PublicationsNote: 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.2 Publications

Enzyme regulationi

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 CaCl2.2 Publications

Kineticsi

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.2 Publications

  1. KM=67 µM for chondroitin 4-sulfate from porcine or bovine trachea (at 37 degrees Celsius and pH 7.6)2 Publications
  2. KM=33 µM for chondroitin 6-sulfate from shark cartilage (at 37 degrees Celsius and pH 7.6)2 Publications
  3. KM=61 µM for dermatan sulfate from porcine intestinal mucosa (at 37 degrees Celsius and pH 7.6)2 Publications
  1. Vmax=77.6 µmol/min/mg enzyme with chondroitin 4-sulfate from bovine trachea as substrate (at 37 degrees Celsius and in 50 mM phosphate at pH 7.6)2 Publications
  2. Vmax=47.4 µmol/min/mg enzyme with chondroitin 6-sulfate from shark cartilage as substrate (at 37 degrees Celsius and in 50 mM phosphate at pH 7.6)2 Publications
  3. Vmax=14.4 µmol/min/mg enzyme with chondroitin 2,6-sulfate from skate cartilage as substrate (at 37 degrees Celsius and in 50 mM phosphate at pH 7.6)2 Publications
  4. Vmax=28.5 µmol/min/mg enzyme with chondroitin 4,6-sulfate from squid cartilage as substrate (at 37 degrees Celsius and in 50 mM phosphate at pH 7.6)2 Publications
  5. Vmax=9.1 µmol/min/mg enzyme with dermatan sulfate from porcine intestinal mucosa as substrate (at 37 degrees Celsius and in 50 mM phosphate at pH 7.6)2 Publications

pH dependencei

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.2 Publications

Temperature dependencei

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.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi24 – 241Calcium1 Publication
Metal bindingi26 – 261Calcium1 Publication
Metal bindingi50 – 501Calcium; via carbonyl oxygen1 Publication
Metal bindingi53 – 531Calcium; via carbonyl oxygen1 Publication
Metal bindingi161 – 1611Calcium1 Publication
Sitei172 – 1721Important for catalytic activity against all substrates1 Publication
Sitei344 – 3441Important for catalytic activity against dermatan sulfate substrate2 Publications
Active sitei345 – 3451Proton acceptor2 Publications
Active sitei454 – 4541Proton acceptor2 Publications
Active sitei461 – 4611Proton donor2 Publications
Sitei514 – 5141Transition state stabilizer1 Publication
Sitei628 – 6281Important for catalytic activity against all substrates2 Publications

GO - Molecular functioni

  • calcium ion binding Source: UniProtKB
  • carbohydrate binding Source: InterPro
  • chondroitin-sulfate-ABC endolyase activity Source: InterPro
  • chondroitin-sulfate-ABC exolyase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB

GO - Biological processi

  • carbohydrate metabolic process Source: UniProtKB-KW
  • dermatan sulfate catabolic process Source: UniProtKB
  • glycosaminoglycan catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Calcium, Metal-binding

Protein family/group databases

CAZyiPL8. Polysaccharide Lyase Family 8.

Names & Taxonomyi

Protein namesi
Recommended name:
Chondroitin sulfate ABC exolyase1 PublicationImported (EC:4.2.2.212 Publications)
Alternative name(s):
Chondroitin ABC exoeliminaseBy similarity
Chondroitin ABC lyase II1 PublicationBy similarity
Chondroitin sulfate ABC lyase II1 PublicationBy similarity
Short name:
ChS ABC lyase IIBy similarity
Chondroitinase ABC II1 PublicationBy similarity
Short name:
cABC IIBy similarity
Exochondroitinase ABCBy similarity
Gene namesi
Name:chonabc
OrganismiBacteroides thetaiotaomicron
Taxonomic identifieri818 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesBacteroidaceaeBacteroides

Subcellular locationi

  • Periplasm By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi172 – 1721R → A: Loss of activity against all substrates. 1 Publication
Mutagenesisi173 – 1731Q → A: Reduced activity against all substrates by a factor of about 2-10. 1 Publication
Mutagenesisi267 – 2671R → A: Reduced activity against all substrates by a factor of about 2-10. 1 Publication
Mutagenesisi344 – 3441H → A: No 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. 2 Publications
Mutagenesisi344 – 3441H → D or E: Loss of activity against all substrates. 2 Publications
Mutagenesisi344 – 3441H → N: Retains 5-25% catalytic efficiency against all substrates. 2 Publications
Mutagenesisi344 – 3441H → Q: Retains 5% catalytic efficiency against chondroitin 4-sulfate only. 2 Publications
Mutagenesisi345 – 3451H → A: No activity against dermatan sulfate even after overnight incubation, but still degrades chondroitin sulfate albeit with 10- to 30-fold lower catalytic efficiency. 2 Publications
Mutagenesisi345 – 3451H → D or E: Loss of activity against all substrates. 2 Publications
Mutagenesisi345 – 3451H → N or Q: Low levels of activity against chondroitin sulfate substrates, but no activity against dermatan sulfate. 2 Publications
Mutagenesisi453 – 4531H → A: Slightly reduced activity against all substrates. 2 Publications
Mutagenesisi453 – 4531H → N: Shows no activity against dermatan sulfate while retaining about 10% of its catalytic efficiency against chondroitin 4- and 6-sulfates. 2 Publications
Mutagenesisi454 – 4541H → A, D, N or Q: Loss of activity against all substrates. 2 Publications
Mutagenesisi461 – 4611Y → A: Loss of activity against all substrates. 2 Publications
Mutagenesisi514 – 5141R → A: Loss of activity against all substrates. 1 Publication
Mutagenesisi628 – 6281E → A or D: Loss of activity against all substrates. 2 Publications
Mutagenesisi628 – 6281E → Q: Retains low levels of activity against chondroitin sulfate substrates, but not against dermatan sulfate as substrate. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1414Sequence analysisAdd
BLAST
Chaini15 – 10141000Chondroitin sulfate ABC exolyaseSequence analysisPRO_0000420123Add
BLAST

Proteomic databases

PaxDbiC5G6D7.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi226186.BT_3324.

Structurei

Secondary structure

1
1014
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 293Combined sources
Beta strandi34 – 4613Combined sources
Beta strandi54 – 6714Combined sources
Beta strandi85 – 9612Combined sources
Beta strandi99 – 10810Combined sources
Beta strandi111 – 1199Combined sources
Beta strandi123 – 1319Combined sources
Turni132 – 1354Combined sources
Beta strandi136 – 1383Combined sources
Beta strandi146 – 1505Combined sources
Beta strandi156 – 16914Combined sources
Turni181 – 1866Combined sources
Turni190 – 1923Combined sources
Helixi194 – 1985Combined sources
Helixi211 – 22818Combined sources
Helixi236 – 24712Combined sources
Beta strandi252 – 2543Combined sources
Beta strandi257 – 2593Combined sources
Helixi266 – 2716Combined sources
Turni273 – 2753Combined sources
Helixi283 – 2864Combined sources
Helixi291 – 30616Combined sources
Helixi313 – 33220Combined sources
Helixi346 – 3483Combined sources
Turni349 – 3524Combined sources
Helixi353 – 3586Combined sources
Helixi361 – 3666Combined sources
Helixi370 – 38011Combined sources
Helixi383 – 3864Combined sources
Beta strandi391 – 3933Combined sources
Helixi397 – 4026Combined sources
Helixi404 – 4129Combined sources
Helixi418 – 43518Combined sources
Beta strandi443 – 4453Combined sources
Beta strandi451 – 4533Combined sources
Helixi459 – 47618Combined sources
Helixi485 – 50117Combined sources
Beta strandi502 – 5065Combined sources
Helixi509 – 5113Combined sources
Helixi524 – 5318Combined sources
Helixi544 – 55310Combined sources
Helixi574 – 58512Combined sources
Beta strandi596 – 6005Combined sources
Turni601 – 6044Combined sources
Beta strandi605 – 6106Combined sources
Beta strandi613 – 6186Combined sources
Beta strandi622 – 6243Combined sources
Beta strandi628 – 6303Combined sources
Turni638 – 6414Combined sources
Beta strandi642 – 6487Combined sources
Turni658 – 6625Combined sources
Beta strandi677 – 6793Combined sources
Helixi683 – 6864Combined sources
Beta strandi699 – 7024Combined sources
Beta strandi710 – 7156Combined sources
Turni716 – 7183Combined sources
Beta strandi719 – 7279Combined sources
Beta strandi737 – 7459Combined sources
Beta strandi748 – 75710Combined sources
Beta strandi761 – 77313Combined sources
Helixi777 – 7826Combined sources
Beta strandi790 – 7945Combined sources
Beta strandi800 – 8023Combined sources
Beta strandi808 – 81811Combined sources
Turni820 – 8223Combined sources
Beta strandi825 – 84016Combined sources
Beta strandi842 – 85312Combined sources
Helixi856 – 8649Combined sources
Beta strandi869 – 88214Combined sources
Turni883 – 8864Combined sources
Beta strandi887 – 8948Combined sources
Beta strandi903 – 92927Combined sources
Beta strandi946 – 9483Combined sources
Helixi955 – 9573Combined sources
Turni959 – 9624Combined sources
Beta strandi968 – 9769Combined sources
Beta strandi986 – 9916Combined sources
Beta strandi993 – 100210Combined sources
Beta strandi1007 – 10137Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q1FX-ray2.85A/B1-1014[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polysaccharide lyase 8 family.Sequence analysis

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105TCD. Bacteria.
ENOG410Y18H. LUCA.

Family and domain databases

Gene3Di1.50.10.100. 1 hit.
2.60.120.410. 1 hit.
2.60.220.10. 1 hit.
2.70.98.10. 1 hit.
InterProiIPR008929. Chondroitin_lyas.
IPR024200. Chondroitinase_ABC_I.
IPR011013. Gal_mutarotase_SF_dom.
IPR008979. Galactose-bd-like.
IPR014718. GH-type_carb-bd.
IPR011071. Lyase_8-like_C.
IPR004103. Lyase_8_C.
IPR003159. Lyase_8_central_dom.
IPR012329. Lyase_8_N.
IPR015177. Lyase_catalyt.
IPR015176. Lyase_N.
[Graphical view]
PfamiPF02278. Lyase_8. 1 hit.
PF09093. Lyase_catalyt. 1 hit.
PF09092. Lyase_N. 1 hit.
[Graphical view]
PIRSFiPIRSF034515. Chondroitinase. 1 hit.
SUPFAMiSSF48230. SSF48230. 1 hit.
SSF49785. SSF49785. 1 hit.
SSF49863. SSF49863. 1 hit.
SSF74650. SSF74650. 1 hit.

Sequencei

Sequence statusi: Complete.

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

C5G6D7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLILSFLCPA FLNAQIVTDE RMFSFEEPQL PACITGVQSQ LGISGAHYKD
60 70 80 90 100
GKHSLEWTFE PNGRLELRKD LKFEKKDPTG KDLYLSAFIV WIYNEQPQDA
110 120 130 140 150
AIEFEFLKDG RKCASFPFGI NFKGWRAAWV CYERDMQGTP EEGMNELRIV
160 170 180 190 200
APDAKGRLFI DHLITATKVD ARQQTADLQV PFVNAGTTNH WLVLYKHSLL
210 220 230 240 250
KPDIELTPVS DKQRQEMKLL EKRFRDMIYT KGKVTEKEAE TIRKKYDLYQ
260 270 280 290 300
ITYKDGQVSG VPVFMVRASE AYERMIPDWD KDMLTKMGIE MRAYFDLMKR
310 320 330 340 350
IAVAYNNSEA GSPIRKEMRR KFLAMYDHIT DQGVAYGSCW GNIHHYGYSV
360 370 380 390 400
RGLYPAYFLM KDVLREEGKL LEAERTLRWY AITNEVYPKP EGNGIDMDSF
410 420 430 440 450
NTQTTGRIAS ILMMEDTPEK LQYLKSFSRW IDYGCRPAPG LAGSFKVDGG
460 470 480 490 500
AFHHRNNYPA YAVGGLDGAT NMIYLFSRTS LAVSELAHRT VKDVLLAMRF
510 520 530 540 550
YCNKLNFPLS MSGRHPDGKG KLVPMHYAIM AIAGTPDGKG DFDKEMASAY
560 570 580 590 600
LRLVSSDSSS AEQAPEYMPK VSNAQERKIA KRLVENGFRA EPDPQGNLSL
610 620 630 640 650
GYGCVSVQRR ENWSAVARGH SRYLWAAEHY LGHNLYGRYL AHGSLQILTA
660 670 680 690 700
PPGQTVTPTT SGWQQEGFDW NRIPGVTSIH LPLDLLKANV LNVDTFSGME
710 720 730 740 750
EMLYSDEAFA GGLSQGKMNG NFGMKLHEHD KYNGTHRARK SFHFIDGMIV
760 770 780 790 800
CLGSDIENTN MDYPTETTIF QLAVTDKAAH DYWKNNAGEG KVWMDHLGTG
810 820 830 840 850
YYVPVAARFE KNFPQYSRMQ DTGKETKGDW VSLIIDHGKA PKAGSYEYAI
860 870 880 890 900
LPGTDRKTMT AFAKKPAYSV LQQDRNAHIL ESPSDRITSY VLFETPQSLL
910 920 930 940 950
PGGLLQRTDT SCLVMVRKES ADKVLLTVAQ PDLALYRGPS DEAFDKDGKR
960 970 980 990 1000
MERSIYSRPW IDNESGEIPV TVTLKGRWKV VETPYCKVVS EDKKQTVLRF
1010
LCKDGASYEV ELEK
Length:1,014
Mass (Da):114,921
Last modified:October 31, 2012 - v2
Checksum:i10C46B91CF02A44A
GO

Sequence cautioni

The sequence ABV21364 differs from that shown.Cloning artifact.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF639172 Genomic DNA. Translation: ABV21364.1. Sequence problems.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF639172 Genomic DNA. Translation: ABV21364.1. Sequence problems.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q1FX-ray2.85A/B1-1014[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226186.BT_3324.

Protein family/group databases

CAZyiPL8. Polysaccharide Lyase Family 8.

Proteomic databases

PaxDbiC5G6D7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105TCD. Bacteria.
ENOG410Y18H. LUCA.

Family and domain databases

Gene3Di1.50.10.100. 1 hit.
2.60.120.410. 1 hit.
2.60.220.10. 1 hit.
2.70.98.10. 1 hit.
InterProiIPR008929. Chondroitin_lyas.
IPR024200. Chondroitinase_ABC_I.
IPR011013. Gal_mutarotase_SF_dom.
IPR008979. Galactose-bd-like.
IPR014718. GH-type_carb-bd.
IPR011071. Lyase_8-like_C.
IPR004103. Lyase_8_C.
IPR003159. Lyase_8_central_dom.
IPR012329. Lyase_8_N.
IPR015177. Lyase_catalyt.
IPR015176. Lyase_N.
[Graphical view]
PfamiPF02278. Lyase_8. 1 hit.
PF09093. Lyase_catalyt. 1 hit.
PF09092. Lyase_N. 1 hit.
[Graphical view]
PIRSFiPIRSF034515. Chondroitinase. 1 hit.
SUPFAMiSSF48230. SSF48230. 1 hit.
SSF49785. SSF49785. 1 hit.
SSF49863. SSF49863. 1 hit.
SSF74650. SSF74650. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCABC2_BACT4
AccessioniPrimary (citable) accession number: C5G6D7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2012
Last sequence update: October 31, 2012
Last modified: September 7, 2016
This is version 25 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.