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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

Manual assertion based on experiment ini

  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)DescriptionActionsGraphical viewLength
Metal bindingi24Calcium1 Publication1
Metal bindingi26Calcium1 Publication1
Metal bindingi50Calcium; via carbonyl oxygen1 Publication1
Metal bindingi53Calcium; via carbonyl oxygen1 Publication1
Metal bindingi161Calcium1 Publication1
Sitei172Important for catalytic activity against all substrates1 Publication1
Sitei344Important for catalytic activity against dermatan sulfate substrate2 Publications1
Active sitei345Proton acceptor2 Publications1
Active sitei454Proton acceptor2 Publications1
Active sitei461Proton donor2 Publications1
Sitei514Transition state stabilizer1 Publication1
Sitei628Important for catalytic activity against all substrates2 Publications1

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)DescriptionActionsGraphical viewLength
Mutagenesisi172R → A: Loss of activity against all substrates. 1 Publication1
Mutagenesisi173Q → A: Reduced activity against all substrates by a factor of about 2-10. 1 Publication1
Mutagenesisi267R → A: Reduced activity against all substrates by a factor of about 2-10. 1 Publication1
Mutagenesisi344H → 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 Publications1
Mutagenesisi344H → D or E: Loss of activity against all substrates. 2 Publications1
Mutagenesisi344H → N: Retains 5-25% catalytic efficiency against all substrates. 2 Publications1
Mutagenesisi344H → Q: Retains 5% catalytic efficiency against chondroitin 4-sulfate only. 2 Publications1
Mutagenesisi345H → 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 Publications1
Mutagenesisi345H → D or E: Loss of activity against all substrates. 2 Publications1
Mutagenesisi345H → N or Q: Low levels of activity against chondroitin sulfate substrates, but no activity against dermatan sulfate. 2 Publications1
Mutagenesisi453H → A: Slightly reduced activity against all substrates. 2 Publications1
Mutagenesisi453H → N: Shows no activity against dermatan sulfate while retaining about 10% of its catalytic efficiency against chondroitin 4- and 6-sulfates. 2 Publications1
Mutagenesisi454H → A, D, N or Q: Loss of activity against all substrates. 2 Publications1
Mutagenesisi461Y → A: Loss of activity against all substrates. 2 Publications1
Mutagenesisi514R → A: Loss of activity against all substrates. 1 Publication1
Mutagenesisi628E → A or D: Loss of activity against all substrates. 2 Publications1
Mutagenesisi628E → Q: Retains low levels of activity against chondroitin sulfate substrates, but not against dermatan sulfate as substrate. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 14Sequence analysisAdd BLAST14
ChainiPRO_000042012315 – 1014Chondroitin sulfate ABC exolyaseSequence analysisAdd BLAST1000

Proteomic databases

PaxDbiC5G6D7.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi226186.BT_3324.

Structurei

Secondary structure

11014
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi27 – 29Combined sources3
Beta strandi34 – 46Combined sources13
Beta strandi54 – 67Combined sources14
Beta strandi85 – 96Combined sources12
Beta strandi99 – 108Combined sources10
Beta strandi111 – 119Combined sources9
Beta strandi123 – 131Combined sources9
Turni132 – 135Combined sources4
Beta strandi136 – 138Combined sources3
Beta strandi146 – 150Combined sources5
Beta strandi156 – 169Combined sources14
Turni181 – 186Combined sources6
Turni190 – 192Combined sources3
Helixi194 – 198Combined sources5
Helixi211 – 228Combined sources18
Helixi236 – 247Combined sources12
Beta strandi252 – 254Combined sources3
Beta strandi257 – 259Combined sources3
Helixi266 – 271Combined sources6
Turni273 – 275Combined sources3
Helixi283 – 286Combined sources4
Helixi291 – 306Combined sources16
Helixi313 – 332Combined sources20
Helixi346 – 348Combined sources3
Turni349 – 352Combined sources4
Helixi353 – 358Combined sources6
Helixi361 – 366Combined sources6
Helixi370 – 380Combined sources11
Helixi383 – 386Combined sources4
Beta strandi391 – 393Combined sources3
Helixi397 – 402Combined sources6
Helixi404 – 412Combined sources9
Helixi418 – 435Combined sources18
Beta strandi443 – 445Combined sources3
Beta strandi451 – 453Combined sources3
Helixi459 – 476Combined sources18
Helixi485 – 501Combined sources17
Beta strandi502 – 506Combined sources5
Helixi509 – 511Combined sources3
Helixi524 – 531Combined sources8
Helixi544 – 553Combined sources10
Helixi574 – 585Combined sources12
Beta strandi596 – 600Combined sources5
Turni601 – 604Combined sources4
Beta strandi605 – 610Combined sources6
Beta strandi613 – 618Combined sources6
Beta strandi622 – 624Combined sources3
Beta strandi628 – 630Combined sources3
Turni638 – 641Combined sources4
Beta strandi642 – 648Combined sources7
Turni658 – 662Combined sources5
Beta strandi677 – 679Combined sources3
Helixi683 – 686Combined sources4
Beta strandi699 – 702Combined sources4
Beta strandi710 – 715Combined sources6
Turni716 – 718Combined sources3
Beta strandi719 – 727Combined sources9
Beta strandi737 – 745Combined sources9
Beta strandi748 – 757Combined sources10
Beta strandi761 – 773Combined sources13
Helixi777 – 782Combined sources6
Beta strandi790 – 794Combined sources5
Beta strandi800 – 802Combined sources3
Beta strandi808 – 818Combined sources11
Turni820 – 822Combined sources3
Beta strandi825 – 840Combined sources16
Beta strandi842 – 853Combined sources12
Helixi856 – 864Combined sources9
Beta strandi869 – 882Combined sources14
Turni883 – 886Combined sources4
Beta strandi887 – 894Combined sources8
Beta strandi903 – 929Combined sources27
Beta strandi946 – 948Combined sources3
Helixi955 – 957Combined sources3
Turni959 – 962Combined sources4
Beta strandi968 – 976Combined sources9
Beta strandi986 – 991Combined sources6
Beta strandi993 – 1002Combined sources10
Beta strandi1007 – 1013Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Q1FX-ray2.85A/B1-1014[»]
SMRiC5G6D7.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Q1FX-ray2.85A/B1-1014[»]
SMRiC5G6D7.
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: November 2, 2016
This is version 26 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.