3WN6 | pdb_00003wn6

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

PDB DOI: https://doi.org/10.2210/pdb3WN6/pdb

Classification: HYDROLASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-12-05 Released: 2014-09-10
Deposition Author(s): Ochiai, A., Sugai, H., Harada, K., Tanaka, S., Ishiyama, Y., Ito, K., Tanaka, T., Uchiumi, T., Taniguchi, M., Mitsui, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.243 (Depositor), 0.261 (DCC)
R-Value Work:
0.199 (Depositor), 0.219 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 25036124 Search on PubMed
DOI: https://doi.org/10.1080/09168451.2014.917261
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 184.32 kDa
Atom Count: 14,765
Modeled Residue Count: 1,616
Deposited Residue Count: 1,616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase	A, B, C, D	404	Oryza sativa Japonica Group	Mutation(s): 1 Gene Names: AMY1.1, AMY1A EC: 3.2.1.1
UniProt
Find proteins for P17654 (Oryza sativa subsp. japonica) Explore P17654 Go to UniProtKB: P17654
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17654
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain HA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain IA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D]	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		Interactions Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D]	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		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain E [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	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		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.243 (Depositor), 0.261 (DCC)
R-Value Work: 0.199 (Depositor), 0.219 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.917	α = 90
b = 125.277	β = 90.2
c = 96.642	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description