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: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    1OJM, 1OJN, 1OJO, 1OJP

  • 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 substrates ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYALURONATE LYASEA731Streptococcus pneumoniaeMutation(s): 0 
EC: 4.2.2.1
UniProt
Find proteins for Q54873 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q54873 
Go to UniProtKB:  Q54873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54873
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G73490KK
GlyCosmos:  G73490KK
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.912α = 90
b = 104.2β = 90
c = 101.499γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-30
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary