7XOI

Aspergillus sojae alpha-glucosidase AsojAgdL in complex with trehalose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for proteolytic processing of Aspergillus sojae alpha-glucosidase L with strong transglucosylation activity.

Ding, Y.Oyagi, A.Miyasaka, Y.Kozono, T.Sasaki, N.Kojima, Y.Yoshida, M.Matsumoto, Y.Yasutake, N.Nishikawa, A.Tonozuka, T.

(2022) J Struct Biol 214: 107874-107874

  • DOI: https://doi.org/10.1016/j.jsb.2022.107874
  • Primary Citation of Related Structures:  
    7XOI

  • PubMed Abstract: 

    An α-glucosidase from Aspergillus sojae, AsojAgdL, exhibits strong transglucosylation activity to produce α-1,6-glucosidic linkages. The most remarkable structural feature of AsojAgdL is that residues 457-560 of AsojAgdL (designated the NC sequence) is not conserved in other glycoside hydrolase family 31 enzymes, and part of this NC sequence is proteolytically cleaved during its maturation. In this study, the enzyme was expressed in Pichia pastoris, and electrophoretic analysis indicated that the recombinant enzyme, rAsojAgdL, consisted of two polypeptide chains, as observed in the case of the enzyme produced in an Aspergillus strain. The crystal structure of rAsojAgdL was determined in complex with the substrate analog trehalose. Electron density corresponding to residues 496-515 of the NC sequence was not seen, and there were no α-helices or β-strands except for a short α-helix in the structures of residues 457-495 and residues 516-560, both of which belong to the NC sequence. The residues 457-495 and the residues 516-560 both formed extra components of the catalytic domain. The residues 457-495 constituted the entrance of the catalytic pocket of rAsojAgdL, and Gly467, Asp468, Pro469, and Pro470 in the NC sequence were located within 4 Å of Trp400, a key residue involved in binding of the substrate. The results suggest that the proteolytic processing of the NC sequence is related to the formation of the catalytic pocket of AsojAgdL.


  • Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-glucosidase N-terminal polypeptide
A, C, E, G, I
A, C, E, G, I, K, M, O
548Aspergillus sojae NBRC 4239Mutation(s): 0 
EC: 3.2.1.20
UniProt
Find proteins for A0A5N6DPG0 (Aspergillus parasiticus)
Explore A0A5N6DPG0 
Go to UniProtKB:  A0A5N6DPG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5N6DPG0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-glucosidase C-terminal polypeptide
B, D, F, H, J
B, D, F, H, J, L, N, P
445Aspergillus sojae NBRC 4239Mutation(s): 0 
EC: 3.2.1.20
UniProt
Find proteins for A0A5N6EXS6 (Aspergillus novoparasiticus)
Explore A0A5N6EXS6 
Go to UniProtKB:  A0A5N6EXS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5N6EXS6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
HA [auth h],
LA [auth l],
PA [auth p],
R,
DA [auth d],
HA [auth h],
LA [auth l],
PA [auth p],
R,
TA [auth t],
V,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
FA [auth f],
JA [auth j],
NA [auth n],
RA [auth r],
BA [auth b],
FA [auth f],
JA [auth j],
NA [auth n],
RA [auth r],
T,
VA [auth v],
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth G]
AD [auth M]
BC [auth G]
BD [auth M]
AB [auth A],
AC [auth G],
AD [auth M],
BC [auth G],
BD [auth M],
CD [auth M],
DB [auth B],
DD [auth M],
EB [auth B],
EC [auth H],
FB [auth C],
FC [auth H],
GB [auth C],
GC [auth H],
GD [auth N],
HB [auth C],
HC [auth I],
HD [auth N],
IB [auth C],
IC [auth I],
ID [auth O],
JB [auth C],
JC [auth I],
JD [auth O],
KC [auth I],
KD [auth O],
LC [auth I],
LD [auth O],
MB [auth D],
MD [auth O],
NB [auth D],
OB [auth E],
OC [auth J],
PB [auth E],
PC [auth J],
PD [auth P],
QB [auth E],
QC [auth J],
QD [auth P],
RB [auth E],
RC [auth K],
SB [auth E],
SC [auth K],
TC [auth K],
VB [auth F],
WA [auth A],
WB [auth F],
WC [auth L],
XA [auth A],
XB [auth G],
XC [auth L],
YA [auth A],
YB [auth G],
YC [auth L],
ZA [auth A],
ZB [auth G],
ZC [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
CB [auth B]
CC [auth G]
ED [auth M]
KB [auth C]
MC [auth I]
CB [auth B],
CC [auth G],
ED [auth M],
KB [auth C],
MC [auth I],
OD [auth P],
TB [auth E],
VC [auth L]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BB [auth B]
DC [auth H]
FD [auth N]
LB [auth D]
NC [auth J]
BB [auth B],
DC [auth H],
FD [auth N],
LB [auth D],
NC [auth J],
ND [auth P],
UB [auth F],
UC [auth L]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.325α = 90.58
b = 106.036β = 90.06
c = 206.366γ = 92.2
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-06-15 
  • Deposition Author(s): Tonozuka, T.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20K05956

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description