Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.06 kDa 
• Atom Count: 3,672 
• Modelled Residue Count: 436 
• Deposited Residue Count: 472 
• Unique protein chains: 1

 1U8X

CRYSTAL STRUCTURE OF GLVA FROM BACILLUS SUBTILIS, A METAL-REQUIRING, NAD-DEPENDENT 6-PHOSPHO-ALPHA-GLUCOSIDASE

• PDB DOI:  https://doi.org/10.2210/pdb1U8X/pdb
• Entry: 1U8X supersedes: 1NRH

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-08-09 Released: 2004-08-24 
• Deposition Author(s): Rajan, S.S., Yang, X., Collart, F., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Novel Catalytic Mechanism of Glycoside Hydrolysis Based on the Structure of an NAD(+)/Mn(2+)-Dependent Phospho-alpha-Glucosidase from Bacillus subtilis.

Rajan, S.S., Yang, X., Collart, F., Yip, V.L., Withers, S.G., Varrot, A., Thompson, J., Davies, G.J., Anderson, W.F.

(2004) Structure 12: 1619-1629

• PubMed: 15341727 
• DOI: https://doi.org/10.1016/j.str.2004.06.020
• Primary Citation of Related Structures:  
  1U8X


• PubMed Abstract: 
  

GlvA, a 6-phospho-alpha-glucosidase from Bacillus subtilis, catalyzes the hydrolysis of maltose-6'-phosphate and belongs to glycoside hydrolase family GH4. GH4 enzymes are unique in their requirement for NAD(H) and a divalent metal for activity. We have determined the crystal structure of GlvA in complex with its ligands to 2.05 A resolution. Analyses of the active site architecture, in conjunction with mechanistic studies and precedent from the nucleotide diphosphate hexose dehydratases and other systems, suggest a novel mechanism of glycoside hydrolysis by GlvA that involves both the NAD(H) and the metal.

---

Organizational Affiliation: 

Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-6'-phosphate glucosidase	A [auth X]	472	Bacillus subtilis	Mutation(s): 17  Gene Names: glvA, glvG, glv-1 EC: 3.2.1.122
UniProt
Find proteins for P54716 (Bacillus subtilis (strain 168)) Explore P54716  Go to UniProtKB:  P54716

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth X]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
G6P	B [auth X]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
MN	C [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.604	α = 90
b = 102.017	β = 90
c = 144.748	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-24 
Deposition Author(s): Rajan, S.S., Yang, X., Collart, F., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 1NRH

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary