245,392
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

1OBB|pdb_00001obb

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

PDB DOI: https://doi.org/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 (Depositor), 0.226 (DCC)
R-Value Work:
0.199 (Depositor), 0.188 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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 Biological Chem 278: 19151

PubMed: 12588867 Search on PubMed
DOI: https://doi.org/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.

Macromolecule Content

Total Structure Weight: 112.32 kDa
Atom Count: 8,523
Modeled Residue Count: 956
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCOSIDASE	A,B	480	Thermotoga maritima MSB8	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O33830
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on 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 Query on PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235 (Depositor), 0.226 (DCC)
R-Value Work: 0.199 (Depositor), 0.188 (DCC)
R-Value Observed: 0.199 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-05-21

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.1: 2024-10-16
Changes: Data collection, Database references, Structure summary