Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 112.32 kDa 
• Atom Count: 8523 
• Modelled Residue Count: 956 
• Deposited Residue Count: 960 
• Unique protein chains: 1

1OBB

alpha-glucosidase A, AglA, from Thermotoga maritima in complex with maltose and NAD+

• PDB DOI: 10.2210/pdb1OBB/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-29 Released: 2003-05-21 
• Deposition Author(s): Lodge, J.A., Maier, T., Liebl, W., Hoffmann, V., Strater, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Crystal Structure of Thermotoga Maritima Alpha-Glucosidase Agla Defines a New Clan of Nad+-Dependent Glycosidases

Lodge, J.A., Maier, T., Liebl, W., Hoffmann, V., Strater, N.

(2003) J Biol Chem 278: 19151

• PubMed: 12588867 
• DOI: 10.1074/jbc.M211626200
• Primary Citation of Related Structures:  
  1OBB


• PubMed Abstract: 
  

Glycoside hydrolase family 4 represents an unusual group of glucosidases with a requirement for NAD+, divalent metal cations, and reducing conditions. The family is also unique in its inclusion of both alpha- and beta-specific enzymes. The alpha-glucosidase A, AglA, from Thermotoga maritima is a typical glycoside hydrolase family 4 enzyme, requiring NAD+ and Mn2+ as well as strongly reducing conditions for activity. Here we present the crystal structure of the protein complexed with NAD+ and maltose, refined at a resolution of 1.9 A. The NAD+ is bound to a typical Rossman fold NAD+-binding site, and the nicotinamide moiety is localized close to the maltose substrate. Within the active site the conserved Cys-174 and surrounding histidines are positioned to play a role in the hydrolysis reaction. The electron density maps indicate that Cys-174 is oxidized to a sulfinic acid. Most likely, the strongly reducing conditions are necessary to reduce the oxidized cysteine side chain. Notably, the canonical set of catalytic acidic residues common to other glucosidases is not present in the active site. This, combined with a high structural homology to NAD-dependent dehydrogenases, suggests an unusual and possibly unique mechanism of action for a glycoside-hydrolyzing enzyme.

---

Organizational Affiliation: 

Institut für Chemie, Takustrasse 6, Freie Universität Berlin, D-14195 Berlin.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCOSIDASE	A, B	480	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: aglA, TM_1834 EC: 3.2.1.20
UniProt
Find proteins for O33830 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore O33830  Go to UniProtKB:  O33830

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75	α = 90
b = 85.7	β = 106
c = 83.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-29 
• Released Date: 2003-05-21 
Deposition Author(s): Lodge, J.A., Maier, T., Liebl, W., Hoffmann, V., Strater, N.

Revision History  

• Version 1.0: 2003-05-21
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2019-04-10
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary