PDBsum entry 1hm2

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Lyase PDB id
Jmol PyMol
Protein chain
674 a.a. *
Waters ×313
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Active site of chondroitinase ac lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis
Structure: Chondroitinase ac. Chain: a. Engineered: yes
Source: Pedobacter heparinus. Organism_taxid: 984. Expressed in: pedobacter heparinus. Expression_system_taxid: 984
2.00Å     R-factor:   0.233     R-free:   0.270
Authors: W.Huang,L.Boju,L.Tkalec,H.Su,H.O.Yang,N.S.Gunay, R.J.Linhardt,Y.S.Kim,A.Matte,M.Cygler
Key ref:
W.Huang et al. (2001). Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis. Biochemistry, 40, 2359-2372. PubMed id: 11327856 DOI: 10.1021/bi0024254
04-Dec-00     Release date:   02-May-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q59288  (CSLA_PEDHD) -  Chondroitinase-AC
700 a.a.
674 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Chondroitin Ac lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Eliminative degradation of polysaccharides containing 1,4-beta-D- hexosaminyl and 1,3-beta-D-glucuronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1021/bi0024254 Biochemistry 40:2359-2372 (2001)
PubMed id: 11327856  
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, M.Cygler.
The crystal structures of Flavobacterium heparinium chondroitin AC lyase (chondroitinase AC; EC bound to dermatan sulfate hexasaccharide (DS(hexa)), tetrasaccharide (DS(tetra)), and hyaluronic acid tetrasaccharide (HA(tetra)) have been refined at 2.0, 2.0, and 2.1 A resolution, respectively. The structure of the Tyr234Phe mutant of AC lyase bound to a chondroitin sulfate tetrasaccharide (CS(tetra)) has also been determined to 2.3 A resolution. For each of these complexes, four (DS(hexa) and CS(tetra)) or two (DS(tetra) and HA(tetra)) ordered sugars are visible in electron density maps. The lyase AC DS(hexa) and CS(tetra) complexes reveal binding at four subsites, -2, -1, +1, and +2, within a narrow and shallow protein channel. We suggest that subsites -2 and -1 together represent the substrate recognition area, +1 is the catalytic subsite and +1 and +2 together represent the product release area. The putative catalytic site is located between the substrate recognition area and the product release area, carrying out catalysis at the +1 subsite. Four residues near the catalytic site, His225, Tyr234, Arg288, and Glu371 together form a catalytic tetrad. The mutations His225Ala, Tyr234Phe, Arg288Ala, and Arg292Ala, revealed residual activity for only the Arg292Ala mutant. Structural data indicate that Arg292 is primarily involved in recognition of the N-acetyl and sulfate moieties of galactosamine, but does not participate directly in catalysis. Candidates for the general base, removing the proton attached to C-5 of the glucuronic acid at the +1 subsite, are Tyr234, which could be transiently deprotonated during catalysis, or His225. Tyrosine 234 is a candidate to protonate the leaving group. Arginine 288 likely contributes to charge neutralization and stabilization of the enolate anion intermediate during catalysis.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
18849565 V.Prabhakar, I.Capila, V.Soundararajan, R.Raman, and R.Sasisekharan (2009).
Recombinant Expression, Purification, and Biochemical Characterization of Chondroitinase ABC II from Proteus vulgaris.
  J Biol Chem, 284, 974-982.  
18574239 H.J.Rozeboom, T.M.Bjerkan, K.H.Kalk, H.Ertesvåg, S.Holtan, F.L.Aachmann, S.Valla, and B.W.Dijkstra (2008).
Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
  J Biol Chem, 283, 23819-23828.
PDB codes: 2pyg 2pyh
18256495 K.Murata, S.Kawai, B.Mikami, and W.Hashimoto (2008).
Superchannel of bacteria: biological significance and new horizons.
  Biosci Biotechnol Biochem, 72, 265-277.  
16521140 C.S.Rye, A.Matte, M.Cygler, and S.G.Withers (2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
  Chembiochem, 7, 631-637.  
16565082 D.Shaya, A.Tocilj, Y.Li, J.Myette, G.Venkataraman, R.Sasisekharan, and M.Cygler (2006).
Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
  J Biol Chem, 281, 15525-15535.
PDB codes: 2fuq 2fut
16834555 R.Sasisekharan, R.Raman, and V.Prabhakar (2006).
Glycomics approach to structure-function relationships of glycosaminoglycans.
  Annu Rev Biomed Eng, 8, 181-231.  
16044262 H.X.Xie, P.Nie, M.X.Chang, Y.Liu, and W.J.Yao (2005).
Gene cloning and functional analysis of glycosaminoglycan-degrading enzyme chondroitin AC lyase from Flavobacterium columnare G4.
  Arch Microbiol, 184, 49-55.  
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
15155751 G.Michel, K.Pojasek, Y.Li, T.Sulea, R.J.Linhardt, R.Raman, V.Prabhakar, R.Sasisekharan, and M.Cygler (2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
  J Biol Chem, 279, 32882-32896.
PDB codes: 1ofl 1ofm
15090531 O.Miyake, A.Ochiai, W.Hashimoto, and K.Murata (2004).
Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1.
  J Bacteriol, 186, 2891-2896.  
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
  16233728 W.Hashimoto, M.Yamasaki, T.Itoh, K.Momma, B.Mikami, and K.Murata (2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
  J Biosci Bioeng, 98, 399-413.  
14523022 D.J.Rigden, and M.J.Jedrzejas (2003).
Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action.
  J Biol Chem, 278, 50596-50606.
PDB codes: 1ojm 1ojn 1ojo 1ojp
12475987 W.Hashimoto, H.Nankai, B.Mikami, and K.Murata (2003).
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
  J Biol Chem, 278, 7663-7673.
PDB codes: 1j0m 1j0n
12044176 J.R.Myette, Z.Shriver, T.Kiziltepe, M.W.McLean, G.Venkataraman, and R.Sasisekharan (2002).
Molecular cloning of the heparin/heparan sulfate delta 4,5 unsaturated glycuronidase from Flavobacterium heparinum, its recombinant expression in Escherichia coli, and biochemical determination of its unique substrate specificity.
  Biochemistry, 41, 7424-7434.  
12063249 K.Pojasek, R.Raman, P.Kiley, G.Venkataraman, and R.Sasisekharan (2002).
Biochemical characterization of the chondroitinase B active site.
  J Biol Chem, 277, 31179-31186.  
12130645 L.V.Mello, B.L.De Groot, S.Li, and M.J.Jedrzejas (2002).
Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan.
  J Biol Chem, 277, 36678-36688.
PDB code: 1lxm
12221284 S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, and G.J.Davies (2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
  Proc Natl Acad Sci U S A, 99, 12067-12072.
PDB codes: 1gxm 1gxn 1gxo
11785764 A.J.Day, and J.K.Sheehan (2001).
Hyaluronan: polysaccharide chaos to protein organisation.
  Curr Opin Struct Biol, 11, 617-622.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.