Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.20 kDa 
• Atom Count: 6332 
• Residue Count: 721 
• Unique protein chains: 1

1N7R

Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A/F343V Mutant complex with hexasaccharide hyaluronan

• DOI: 10.2210/pdb1N7R/pdb

• Classification: LYASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-11-16 Released: 2002-12-31 
• Deposition Author(s): Nukui, M., Taylor, K.B., McPherson, D.T., Shigenaga, M., Jedrzejas, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 

Literature

The function of hydrophobic residues in the catalytic cleft of Streptococcus pneumoniae hyaluronate lyase. Kinetic characterization of mutant enzyme forms

Nukui, M., Taylor, K.B., McPherson, D.T., Shigenaga, M., Jedrzejas, M.J.

(2003) J Biol Chem 278: 3079-3088

• PubMed: 12446724 
• DOI: 10.1074/jbc.M204999200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Streptococcus pneumoniae hyaluronate lyase is a surface antigen of this Gram-positive human bacterial pathogen. The primary function of this enzyme is the degradation of hyaluronan, which is a major component of the extracellular matrix of the tissues of vertebrates and of some bacteria. The enzyme degrades its substrate through a beta-elimination process called proton acceptance and donation. The inherent part of this degradation is a processive mode of action of the enzyme degrading hyaluronan into unsaturated disaccharide hyaluronic acid blocks from the reducing to the nonreducing end of the polymer following the initial random endolytic binding to the substrate. The final degradation product is the unsaturated disaccharide hyaluronic acid. The residues of the enzyme that are involved in various aspects of such degradation were identified based on the three-dimensional structures of the native enzyme and its complexes with hyaluronan substrates of various lengths. The catalytic residues were identified to be Asn(349), His(399), and Tyr(408). The residues responsible for the release of the product of the reaction were identified as Glu(388), Asp(398), and Thr(400), and they were termed negative patch. The hydrophobic residues Trp(291), Trp(292), and Phe(343) were found to be responsible for the precise positioning of the substrate for enzyme catalysis and named hydrophobic patch. The comparison of the specific activities and kinetic properties of the wild type and the mutant enzymes involving the hydrophobic patch residues W292A, F343V, W291A/W292A, W292A/F343V, and W291A/W292A/F343V allowed for the characterization of every mutant and for the correlation of the activity and kinetic properties of the enzyme with its structure as well as the mechanism of catalysis.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HYALURONIDASE	A	721	Streptococcus pneumoniae	Mutation(s): 3  EC: 4.2.2.1
Find proteins for Q54873 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54873  Go to UniProtKB:  Q54873

Oligosaccharides

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram
beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.491	α = 90
b = 102.494	β = 90
c = 103.698	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
MADNESS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-16 
• Released Date: 2002-12-31 
Deposition Author(s): Nukui, M., Taylor, K.B., McPherson, D.T., Shigenaga, M., Jedrzejas, M.J.

Revision History 

• Version 1.0: 2002-12-31
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary