Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.54 kDa 
• Atom Count: 10,681 
• Modelled Residue Count: 1,106 
• Deposited Residue Count: 1,117 
• Unique protein chains: 1

 5A56

The structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with 1-O-methyl-T-antigen

• PDB DOI:  https://doi.org/10.2210/pdb5A56/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-16 Released: 2015-09-02 
• Deposition Author(s): Gregg, K.J., Suits, M.D.L., Deng, L., Vocadlo, D.J., Boraston, A.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.178 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

Literature

Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism.

Gregg, K.J., Suits, M.D., Deng, L., Vocadlo, D.J., Boraston, A.B.

(2015) J Biol Chem 290: 25657-25669

• PubMed: 26304114 
• DOI: https://doi.org/10.1074/jbc.M115.680470
• Primary Citation of Related Structures:  
  5A55, 5A56, 5A57, 5A58, 5A59, 5A5A


• PubMed Abstract: 
  

O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.

---

Organizational Affiliation: 

From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6 and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE	A	1,117	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP_0368 EC: 3.2.1.97
UniProt
Find proteins for Q2MGH6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q2MGH6  Go to UniProtKB:  Q2MGH6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside	B	2		N/A
Glycosylation Resources
GlyTouCan:  G70497XY GlyCosmos:  G70497XY

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	G [auth A], H [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.178 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.713	α = 90
b = 121.764	β = 90
c = 139.429	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Gregg, K.J., Suits, M.D.L., Deng, L., Vocadlo, D.J., Boraston, A.B.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2015-10-28
  Changes: Database references
• Version 1.3: 2019-09-25
  Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary