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PDBsum entry 1ojn

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Lyase PDB id
1ojn
Jmol
Contents
Protein chain
723 a.a. *
Ligands
GCD-NG6
SO4 ×4
Waters ×638
* Residue conservation analysis
PDB id:
1ojn
Name: Lyase
Title: Specificity and mechanism of streptococcus pneumoniae hyaluronate lyase: complex of the tyr408phe mutant with 6-sulphated chondroitin disaccharide
Structure: Hyaluronate lyase. Chain: a. Fragment: hyaluronate lyase, residues 285-1009. Synonym: hyaluronidase, hyase. Engineered: yes. Mutation: yes
Source: Streptococcus pneumoniae. Organism_taxid: 1313. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
1.60Å     R-factor:   0.194     R-free:   0.209
Authors: D.J.Rigden,M.J.Jedrzejas
Key ref:
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. PubMed id: 14523022 DOI: 10.1074/jbc.M307596200
Date:
11-Jul-03     Release date:   30-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q54873  (HYSA_STRPN) -  Hyaluronate lyase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1066 a.a.
723 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.2.2.1  - Hyaluronate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hyaluronate = N 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D- glucosamine

=
N
Bound ligand (Het Group name = NG6)
matches with 50.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M307596200 J Biol Chem 278:50596-50606 (2003)
PubMed id: 14523022  
 
 
Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action.
D.J.Rigden, M.J.Jedrzejas.
 
  ABSTRACT  
 
Streptococcus pneumoniae hyaluronate lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades hyaluronan and chondroitin/chondroitin sulfates by cleaving the beta1,4-glycosidic linkage between the glycan units of these polymeric substrates. This degradation helps spreading of this bacterial organism throughout the host tissues and facilitates the disease process caused by pneumococci. The mechanism of this degradative process is based on beta-elimination, is termed proton acceptance and donation, and involves selected residues of a well defined catalytic site of the enzyme. The degradation of hyaluronan alone is thought to proceed through a processive mode of action. The structures of complexes between the enzyme and chondroitin as well as chondroitin sulfate disaccharides allowed for the first detailed insights into these interactions and the mechanism of action on chondroitins. This degradation of chondroitin/chondroitin sulfates is nonprocessive and is selective for the chondroitin sulfates only with certain sulfation patterns. Chondroitin sulfation at the 4-position on the nonreducing site of the linkage to be cleaved or 2-sulfation prevent degradation due to steric clashes with the enzyme. Evolutionary studies suggest that hyaluronate lyases evolved from chondroitin lyases and still retained chondroitin/chondroitin sulfate degradation abilities while being specialized in the degradation of hyaluronan. The more efficient processive degradation mechanism has come to be preferred for the unsulfated substrate hyaluronan.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Structure of S. pneumoniae hyaluronate lyase. a, overall view of S. pneumoniae hyaluronate lyase bound to hyaluronan hexasaccharide (15, 22). The ligand is shown as a ball-and-stick model, and some catalytic site residues mentioned herein are drawn as sticks. Some binding subsites (nomenclature of Ref. 66) are labeled, as are the reducing (R) and nonreducing (NR) ends of the substrate chain. b, close-up view of S. pneumoniae hyaluronate lyase bound to hyaluronan hexasaccharide in a similar orientation to a. A semitransparent molecular surface is shown. The figure was made using PYMOL (83), as were Figs. 3, 4, 5, 6.
Figure 4.
FIG. 4. View of Di0S disaccharide bound to hyaluronate lyase, focusing on the environment of the 2-hydroxyl of the D-glucuronic acid unit (labeled 2) bound in subsite -2 (labeled -2). Cyan spheres represent water molecules, and dashed lines represent potential hydrogen bonds. Introduction of a 2-sulfate group would lead to severe steric clashes.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 50596-50606) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19089975 H.V.Joshi, M.J.Jedrzejas, and B.L.de Groot (2009).
Domain motions of hyaluronan lyase underlying processive hyaluronan translocation.
  Proteins, 76, 30-46.  
19270385 K.Matsuo, H.Namatame, M.Taniguchi, and K.Gekko (2009).
Vacuum-ultraviolet circular dichroism analysis of glycosaminoglycans by synchrotron-radiation spectroscopy.
  Biosci Biotechnol Biochem, 73, 557-561.  
16732155 E.L.Tonnaer, K.Graamans, E.A.Sanders, and J.H.Curfs (2006).
Advances in understanding the pathogenesis of pneumococcal otitis media.
  Pediatr Infect Dis J, 25, 546-552.  
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
16104017 M.J.Jedrzejas, and R.Stern (2005).
Structures of vertebrate hyaluronidases and their unique enzymatic mechanism of hydrolysis.
  Proteins, 61, 227-238.  
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.