1P6W | pdb_00001p6w

Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with the substrate analogue, methyl 4I,4II,4III-tri-thiomaltotetraoside (thio-DP4)

PDB DOI: https://doi.org/10.2210/pdb1P6W/pdb

Classification: HYDROLASE
Organism(s): Hordeum vulgare
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2003-04-30 Released: 2003-10-14
Deposition Author(s): Robert, X., Haser, R., Aghajari, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.216 (Depositor), 0.221 (DCC)
R-Value Work:
0.170 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs

Robert, X., Haser, R., Gottschalk, T.E., Ratajczak, F., Driguez, H., Svensson, B., Aghajari, N.

(2003) Structure 11: 973-984

PubMed: 12906828 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(03)00151-5
Primary Citation Related Structures:
1HT6, 1P6W

PubMed Abstract:
Though the three-dimensional structures of barley alpha-amylase isozymes AMY1 and AMY2 are very similar, they differ remarkably from each other in their affinity for Ca(2+) and when interacting with substrate analogs. A surface site recognizing maltooligosaccharides, not earlier reported for other alpha-amylases and probably associated with the different activity of AMY1 and AMY2 toward starch granules, has been identified. It is located in the C-terminal part of the enzyme and, thus, highlights a potential role of domain C. In order to scrutinize the possible biological significance of this domain in alpha-amylases, a thorough comparison of their three-dimensional structures was conducted. An additional role for an earlier-identified starch granule binding surface site is proposed, and a new calcium ion is reported.

Organizational Affiliation

Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086-CNRS/UCBL1, 7 Passage du Vercors, F-69367 Lyon cedex 07, France.

Macromolecule Content

Total Structure Weight: 46.25 kDa
Atom Count: 3,877
Modeled Residue Count: 404
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Alpha-amylase type A isozyme)	A	405	Hordeum vulgare	Mutation(s): 0 Gene Names: AMY1.1 EC: 3.2.1.1
UniProt
Find proteins for P00693 (Hordeum vulgare) Explore P00693 Go to UniProtKB: P00693
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00693
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside	B	4	N/A	N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G75417ZK GlyCosmos: G75417ZK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose	C, D	2	N/A	N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G09196LL GlyCosmos: G09196LL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.216 (Depositor), 0.221 (DCC)
R-Value Work: 0.170 (Depositor), 0.179 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.43	α = 90
b = 72.1	β = 90
c = 60.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-10-14

Deposition Author(s):

Robert, X.

Haser, R.

Aghajari, N.

Revision History (Full details and data files)

Version 1.0: 2003-10-14
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary