2D0G | pdb_00002d0g

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P5, a pullulan model oligosaccharide

PDB DOI: https://doi.org/10.2210/pdb2D0G/pdb

Classification: HYDROLASE
Organism(s): Thermoactinomyces vulgaris
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-08-02 Released: 2006-07-11
Deposition Author(s): Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.190 (Depositor), 0.186 (DCC)
R-Value Work:
0.150 (Depositor), 0.145 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages

Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

(2005) FEBS J 272: 6145-6153

PubMed: 16302977 Search on PubMed
DOI: https://doi.org/10.1111/j.1742-4658.2005.05013.x
Primary Citation Related Structures:
2D0F, 2D0G, 2D0H

PubMed Abstract:
Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.

Organizational Affiliation

Graduate School of Medicine, Kagawa University, Japan.

Macromolecule Content

Total Structure Weight: 74.52 kDa
Atom Count: 5,737
Modeled Residue Count: 637
Deposited Residue Count: 637
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase I	A	637	Thermoactinomyces vulgaris	Mutation(s): 2 EC: 3.2.1.1 (PDB Primary Data), 3.2.1.135 (UniProt)
UniProt
Find proteins for Q60053 (Thermoactinomyces vulgaris) Explore Q60053 Go to UniProtKB: Q60053
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60053
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)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	10		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G39844GI GlyCosmos: G39844GI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	5		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G95107LS GlyCosmos: G95107LS

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	C	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.190 (Depositor), 0.186 (DCC)
R-Value Work: 0.150 (Depositor), 0.145 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.885	α = 90
b = 50.698	β = 103.43
c = 108.007	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-07-11
Type: Initial release
Version 1.1: 2008-04-30
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: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-11-10
Changes: Database references, Structure summary
Version 2.2: 2024-05-29
Changes: Data collection