5YKB | pdb_00005ykb

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site conformation

PDB DOI: https://doi.org/10.2210/pdb5YKB/pdb
Entry: 5YKB supersedes: 5GTV

Classification: ISOMERASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-10-13 Released: 2017-10-25
Deposition Author(s): Chow, S.Y., Hsieh, Y.C., Liaw, S.H.
Funding Organization(s): Ministry of Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.251 (Depositor), 0.252 (DCC)
R-Value Work:
0.192 (Depositor), 0.199 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology

Chow, S.Y., Wang, Y.L., Hsieh, Y.C., Lee, G.C., Liaw, S.H.

(2017) Acta Crystallogr F Struct Biol Commun 73: 588-594

PubMed: 29095151 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X17014303
Primary Citation Related Structures:
5YKB

PubMed Abstract:
Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.

Organizational Affiliation

Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Taipei 11221, Taiwan.

Macromolecule Content

Total Structure Weight: 260.34 kDa
Atom Count: 17,196
Modeled Residue Count: 2,104
Deposited Residue Count: 2,284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trehalose synthase	A, B, C, D	571	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 4 EC: 5.4.99.16
UniProt
Find proteins for I3NX86 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore I3NX86 Go to UniProtKB: I3NX86
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3NX86
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.251 (Depositor), 0.252 (DCC)
R-Value Work: 0.192 (Depositor), 0.199 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.401	α = 90
b = 132.422	β = 90
c = 196.013	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Chow, S.Y.

Hsieh, Y.C.

Liaw, S.H.

This entry supersedes: 5GTV

Funding Organization	Location	Grant Number
Ministry of Science and Technology	Taiwan	NSC 102-2311-B-010-005

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2017-11-01
Changes: Database references
Version 1.2: 2017-11-15
Changes: Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description