3WN6

Crystal structure of alpha-amylase AmyI-1 from Oryza sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of alpha-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability

Ochiai, A.Sugai, H.Harada, K.Tanaka, S.Ishiyama, Y.Ito, K.Tanaka, T.Uchiumi, T.Taniguchi, M.Mitsui, T.

(2014) Biosci Biotechnol Biochem 78: 989-997

  • DOI: https://doi.org/10.1080/09168451.2014.917261
  • Primary Citation of Related Structures:  
    3WN6

  • PubMed Abstract: 
  • AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases ...

    AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.


    Organizational Affiliation

    a Faculty of Engineering, Department of Materials Science and Technology , Niigata University , Niigata , Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-amylaseA, B, C, D404Oryza sativa Japonica GroupMutation(s): 1 
Gene Names: AMY1.1AMY1AOs02g0765600LOC_Os02g52710OJ1004_A11.13P0539D10.32
EC: 3.2.1.1
UniProt
Find proteins for P17654 (Oryza sativa subsp. japonica)
Explore P17654 
Go to UniProtKB:  P17654
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17654
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
HA [auth D],
J [auth A],
K [auth A],
AA [auth C],
BA [auth C],
HA [auth D],
J [auth A],
K [auth A],
T [auth B]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
IA [auth D],
JA [auth D],
KA [auth D],
L [auth A],
LA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
Q [auth B],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
G [auth A],
N [auth B],
O [auth B],
P [auth B],
V [auth C],
W [auth C],
X [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.917α = 90
b = 125.277β = 90.2
c = 96.642γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release