1OJN

SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 6-SULPHATED CHONDROITIN DISACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Chondroitin and Chondroitin Sulfate Disaccharides: Insights Into Specificity and Mechanism of Action

Rigden, D.J.Jedrzejas, M.J.

(2003) J.Biol.Chem. 278: 50596

  • DOI: 10.1074/jbc.M307596200
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Related Citations: 
    • Structural Basis of Hyaluronan Degradation by Streptococcus Pneumoniae Hyaluronate Lyase
      Li, S.,Kelly, S.J.,Lamani, E.,Ferraroni, M.,Jedrzejas, M.J.
      (2000) Embo J. 19: 1228


    Organizational Affiliation

    Children's Hospital Oakland Research Institute, Oakland, California 94609, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYALURONATE LYASE
A
731Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
EC: 4.2.2.1
Find proteins for Q54873 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q54873
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NG6
Query on NG6

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GALACTOSAMINE 6-SULFATE
C8 H15 N O9 S
WJFVEEAIYIOATH-JAJWTYFOSA-N
 Ligand Interaction
GCD
Query on GCD

Download SDF File 
Download CCD File 
A
4,5-DEHYDRO-D-GLUCURONIC ACID
C6 H8 O6
IAKKJSVSFCTLRY-YKKSOZKNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.912α = 90.00
b = 104.200β = 90.00
c = 101.499γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-30
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance