3EKA

Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose.

Mishra, P.Prem Kumar, R.Ethayathulla, A.S.Singh, N.Sharma, S.Perbandt, M.Betzel, C.Kaur, P.Srinivasan, A.Bhakuni, V.Singh, T.P.

(2009) FEBS J 276: 3392-3402

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.07065.x
  • Primary Citation of Related Structures:  
    2YW0, 3EKA

  • PubMed Abstract: 

    Hyaluronate lyases are a class of endoglycosaminidase enzymes with a high level of complexity and heterogeneity. The main function of the Streptococcus pyogenes bacteriophage protein hyaluronate lyase, HylP2, is to degrade hyaluronan into unsaturated disaccharide units. HylP2 was cloned, over-expressed and purified to homogeneity. The recombinant HylP2 exists as a homotrimer with a molecular mass of approximately 110 kDa under physiological conditions. The HylP2 was crystallized and the crystals were soaked in two separate reservoir solutions containing ascorbic acid and lactose, respectively. The crystal structures of native HylP2 and its two complexes with ascorbic acid and lactose have been determined. HylP2 folds into four distinct domains with a central core consisting of 16 antiparallel beta-strands forming an irregular triangular tube designated as triple-stranded beta-helix. The structures of complexes show that three molecules each of ascorbic acid and lactose bind to protein at the sugar binding groove in the triple-stranded beta-helix domain. Both ascorbic acid and lactose molecules occupy almost identical subsites in the long saccharide binding groove. Both ligands are involved in several hydrogen bonded interactions at each subsite. The binding characteristics and stereochemical properties indicate that Tyr264 may be involved in the catalytic activity of HylP2. The mutation of Tyr264 to Phe264 supports this observation.


  • Organizational Affiliation

    Department of Molecular and Structural Biology, Central Drug Research Institute, Lucknow, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyaluronidase, phage associated332Streptococcus pyogenesMutation(s): 0 
Gene Names: hylP1HYLP2SPy_0701
EC: 4.2.2.1
UniProt
Find proteins for Q9A0M7 (Streptococcus pyogenes serotype M1)
Explore Q9A0M7 
Go to UniProtKB:  Q9A0M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A0M7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ASC PDBBind:  3EKA IC50: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.502α = 90
b = 58.502β = 90
c = 583.54γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary