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Lyase PDB id
1ofm
Jmol
Contents
Protein chain
481 a.a. *
Ligands
MAN-RAM-GCU-XYP-
MXZ-GLA-BGC
ASG-BDP-ASG-DGC
Waters ×806
* Residue conservation analysis
PDB id:
1ofm
Name: Lyase
Title: Crystal structure of chondroitinase b complexed to chondroitin 4-sulfate tetrasaccharide
Structure: Chondroitinase b. Chain: a. Engineered: yes. Other_details: hydroxy-proline at n-terminus glycosylation at ser234
Source: Pedobacter heparinus. Organism_taxid: 984. Atcc: 13125. Expressed in: pedobacter heparinus. Expression_system_taxid: 984
Resolution:
1.80Å     R-factor:   0.142     R-free:   0.183
Authors: G.Michel,M.Cygler
Key ref:
G.Michel et al. (2004). The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. J Biol Chem, 279, 32882-32896. PubMed id: 15155751 DOI: 10.1074/jbc.M403421200
Date:
15-Apr-03     Release date:   19-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
Q46079  (CSLB_PEDHD) -  Chondroitinase-B
Seq:
Struc: 		506 a.a.
481 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.2.2.19  - Chondroitin B lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     lyase activity     2 terms  

 

 
DOI no: 10.1074/jbc.M403421200 J Biol Chem 279:32882-32896 (2004)
PubMed id: 15155751  
 
 
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
G.Michel, K.Pojasek, Y.Li, T.Sulea, R.J.Linhardt, R.Raman, V.Prabhakar, R.Sasisekharan, M.Cygler.
 
  ABSTRACT  
 
Chondroitinase B from Pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. This beta-helical polysaccharide lyase belongs to family PL-6 and cleaves the beta(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. The previously reported structure of its complex with a dermatan sulfate disaccharide product identified the -1 and -2 subsites of the catalytic groove. We present here the structure of chondroitinase B complexed with several dermatan sulfate and chondroitin sulfate oligosaccharides. In particular, the soaking of chondroitinase B crystals with a dermatan sulfate hexasaccharide results in a complex with two dermatan sulfate disaccharide reaction products, enabling the identification of the +2 and +1 subsites. Unexpectedly, this structure revealed the presence of a calcium ion coordinated by sequence-conserved acidic residues and by the carboxyl group of the l-iduronic acid at the +1 subsite. Kinetic and site-directed mutagenesis experiments have subsequently demonstrated that chondroitinase B absolutely requires calcium for its activity, indicating that the protein-Ca(2+)-oligosaccharide complex is functionally relevant. Modeling of an intact tetrasaccharide in the active site of chondroitinase B provided a better understanding of substrate specificity and the role of Ca(2+) in enzymatic activity. Given these results, we propose that the Ca(2+) ion neutralizes the carboxyl moiety of the l-iduronic acid at the cleavage site, whereas the conserved residues Lys-250 and Arg-271 act as Brønsted base and acid, respectively, in the lytic degradation of dermatan sulfate by chondroitinase B.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Chondroitinase B. A, ribbon representation of the ChonB-DShexa complex with the secondary structures colored according to a blue-red gradient from the N to the C terminus. B, view of the molecular surface of ChonB. The three dermatan sulfate oligosaccharides near the active site are shown in a stick representation. The calcium ion is shown as a yellow sphere. This and subsequent figures was prepared using the program PyMOL (DeLano Scientific, pymol.sourceforge.net/). 		Figure 2.
FIG. 2. Fo-Fc electron density map of the dermatan sulfate disaccharides bound to the active site of ChonB and the Ca^2^+-binding site (A) and the dermatan sulfate disaccharide bound on the outer surface of ChonB (B). The oligosaccharides and the Ca^2+ ion were excluded from the calculations of phases.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 32882-32896) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287626 Z.H.Elmabrouk, F.Vincent, M.Zhang, N.L.Smith, J.P.Turkenburg, S.J.Charnock, G.W.Black, and E.J.Taylor (2011).
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations.
  Proteins, 79, 965-974.
PDB codes: 2wco 2wda 2x03
20868223 D.R.Carrillo, C.Parthier, N.Jänckel, J.Grandke, M.Stelter, S.Schilling, M.Boehme, P.Neumann, R.Wolf, H.U.Demuth, M.T.Stubbs, and J.U.Rahfeld (2010).
Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus.
  Biol Chem, 391, 1419-1428.
PDB codes: 3nok 3nol 3nom
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.  
19801541 Y.H.Han, M.L.Garron, H.Y.Kim, W.S.Kim, Z.Zhang, K.S.Ryu, D.Shaya, Z.Xiao, C.Cheong, Y.S.Kim, R.J.Linhardt, Y.H.Jeon, and M.Cygler (2009).
Structural snapshots of heparin depolymerization by heparin lyase I.
  J Biol Chem, 284, 34019-34027.
PDB codes: 3ikw 3ilr 3imn 3in9 3ina
18493641 E.Gemma, O.Meyer, D.Uhrín, and A.N.Hulme (2008).
Enabling methodology for the end functionalization of glycosaminoglycan oligosaccharides.
  Mol Biosyst, 4, 481-495.  
17849372 K.N.Kirschner, A.B.Yongye, S.M.Tschampel, J.González-Outeiriño, C.R.Daniels, B.L.Foley, and R.J.Woods (2008).
GLYCAM06: A generalizable biomolecular force field. Carbohydrates.
  J Comput Chem, 29, 622-655.  
17150374 H.B.Henninger, S.A.Maas, C.J.Underwood, R.T.Whitaker, and J.A.Weiss (2007).
Spatial distribution and orientation of dermatan sulfate in human medial collateral ligament.
  J Struct Biol, 158, 33-45.  
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.  
16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
  Appl Microbiol Biotechnol, 71, 23-33.  
16834555 R.Sasisekharan, R.Raman, and V.Prabhakar (2006).
Glycomics approach to structure-function relationships of glycosaminoglycans.
  Annu Rev Biomed Eng, 8, 181-231.  
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.