2FUZ | pdb_00002fuz

UGL hexagonal crystal structure without glycine and DTT molecules

• PDB DOI: https://doi.org/10.2210/pdb2FUZ/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. GL1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-28 Released: 2006-05-30 
• Deposition Author(s): Itoh, T., Hashimoto, W., Mikami, B., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.188 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1

Itoh, T., Hashimoto, W., Mikami, B., Murata, K.

(2006) Biochem Biophys Res Commun 344: 253-262

• PubMed: 16630576 
• DOI: https://doi.org/10.1016/j.bbrc.2006.03.141
• Primary Citation Related Structures: 
  2FUZ, 2FV0, 2FV1


• PubMed Abstract: 
  

  Bacterial unsaturated glucuronyl hydrolases (UGLs) together with polysaccharide lyases are responsible for the complete depolymerization of mammalian extracellular matrix glycosaminoglycans. UGL acts on various oligosaccharides containing unsaturated glucuronic acid (DeltaGlcA) at the nonreducing terminus and releases DeltaGlcA through hydrolysis. In this study, we demonstrate the substrate recognition mechanism of the UGL of Bacillus sp. GL1 by determining the X-ray crystallographic structure of its substrate-enzyme complexes. The tetrasaccharide-enzyme complex demonstrated that at least four subsites are present in the active pocket. Although several amino acid residues are crucial for substrate binding, the enzyme strongly recognizes DeltaGlcA at subsite -1 through the formation of hydrogen bonds and stacking interactions, and prefers N-acetyl-d-galactosamine and glucose rather than N-acetyl-d-glucosamine as a residue accommodated in subsite +1, due to the steric hindrance.

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Organizational Affiliation: 
• Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.98 kDa 
• Atom Count: 3,604 
• Modeled Residue Count: 377 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unsaturated glucuronyl hydrolase	A	377	Bacillus sp. GL1	Mutation(s): 0  Gene Names: ugl EC: 3.2.1 (PDB Primary Data), 3.2.1.179 (UniProt)
UniProt
Find proteins for Q9RC92 (Bacillus sp. (strain GL1)) Explore Q9RC92  Go to UniProtKB:  Q9RC92

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.188 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.818	α = 90
b = 102.818	β = 90
c = 223.156	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-30 
Deposition Author(s): Itoh, T., Hashimoto, W., Mikami, B., Murata, K.

Revision History  

• Version 1.0: 2006-05-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description