2BRV

Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 70percent saturated malonate.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.302 

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This is version 1.1 of the entry. See complete history. 


Literature

Alternate Structural Conformations of Streptococcus Pneumoniae Hyaluronan Lyase: Insights Into Enzyme Flexibility and Underlying Molecular Mechanism of Action.

Rigden, D.J., Littlejohn, J.E., Joshi, H.V., De Groot, B.L., Jedrzejas, M.J.

(2006) J Mol Biol 358: 1165

  • DOI: 10.1016/j.jmb.2006.02.066
  • Primary Citation of Related Structures:  
    2BRV, 2BRW

  • PubMed Abstract: 

    • Streptococcus pneumoniae hyaluronan lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades several biologically important, information-rich linear polymeric glycans: hyaluronan, unsulfated chondroitin, and some chondroitin sulfates ...

    Streptococcus pneumoniae hyaluronan lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades several biologically important, information-rich linear polymeric glycans: hyaluronan, unsulfated chondroitin, and some chondroitin sulfates. This degradation facilitates spreading of bacteria throughout the host tissues and presumably provides energy and a carbon source for pneumococcal cells. Its beta-elimination catalytic mechanism is an acid/base process termed proton acceptance and donation leading to cleavage of beta-1,4 linkages of the substrates. The degradation of hyaluronan occurs in two stages, initial endolytic cuts are followed by processive exolytic cleavage of one disaccharide at a time. In contrast, the degradation of chondroitins is purely endolytic. Structural studies together with flexibility analyses of two streptococcal enzymes, from S.pneumoniae and Streptococcus agalactiae, allowed for insights into this enzyme's molecular mechanism. Here, two new X-ray crystal structures of the pneumococcal enzyme in novel conformations are reported. These new conformations, complemented by molecular dynamics simulation results, directly confirm the predicted domain motions presumed to facilitate the processive degradative process. One of these new structures resembles the S.agalactiae enzyme conformation, and provides evidence of a uniform mechanistic/dynamic behavior of this protein across different bacteria.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYALURONATE LYASEA [auth X]731Streptococcus 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA
Download Ideal Coordinates CCD File 
B [auth X],
C [auth X],
D [auth X],
E [auth X],
F [auth X],
B [auth X],
C [auth X],
D [auth X],
E [auth X],
F [auth X],
G [auth X]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.302 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.722α = 90
b = 101.052β = 125.12
c = 85.211γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-05
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Advisory, Database references, Derived calculations, Non-polymer description, Other, Version format compliance