2F2H | pdb_00002f2h

Structure of the YicI thiosugar Michaelis complex

PDB DOI: https://doi.org/10.2210/pdb2F2H/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-11-16 Released: 2006-02-28
Deposition Author(s): Kim, Y.-W., Lovering, A.L., Strynadka, N.C.J., Withers, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.225 (Depositor), 0.231 (DCC)
R-Value Work:
0.180 (Depositor), 0.188 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Expanding the Thioglycoligase Strategy to the Synthesis of alpha-linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex

Kim, Y.-W., Lovering, A.L., Chen, H., Kantner, T., McIntosh, L.P., Strynadka, N.C.J., Withers, S.G.

(2006) J Am Chem Soc 128: 2202-2203

PubMed: 16478160 Search on PubMed
DOI: https://doi.org/10.1021/ja057904a
Primary Citation Related Structures:
2F2H

PubMed Abstract:
For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfataricus, catalyze thioglycoligase reactions using alpha-glycosyl fluorides and deoxythioglycosides as donors and acceptors, respectively, in yields up to 86%. In addition, we describe the Michaelis complex of YicI using one of the thioglycosides as a nonhydrolyzable substrate analogue and discuss the structural insights this yields into the specificity and mechanism of family 31 alpha-glycosidases and the molecular basis of an associated genetic disease.

Organizational Affiliation

Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.

Macromolecule Content

Total Structure Weight: 536.21 kDa
Atom Count: 39,799
Modeled Residue Count: 4,638
Deposited Residue Count: 4,638
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative family 31 glucosidase yicI	A, B, C, D, E A, B, C, D, E, F	773	Escherichia coli	Mutation(s): 0 Gene Names: yicI EC: 3.2.1.177
UniProt
Find proteins for P31434 (Escherichia coli (strain K12)) Explore P31434 Go to UniProtKB: P31434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31434
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XTG Query on XTG Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain H [auth A] SDF format, chain LA [auth F] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	EA [auth E] H [auth A] LA [auth F] MA [auth F] N [auth B] EA [auth E], H [auth A], LA [auth F], MA [auth F], N [auth B], S [auth C], Y [auth D]	4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE C₁₇ H₂₃ N O₁₁ S HQYVHBCTLFPWRQ-ZMFOIVQCSA-N		Interactions Focus chain EA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]
MPO Query on MPO Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain KA [auth F] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	DA [auth E], KA [auth F], M [auth B], R [auth C], X [auth D]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain KA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain DA [auth E] Focus chain KA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain IA [auth F] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain JA [auth F] SDF format, chain HA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain JA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain JA [auth F] mmCIF format, chain HA [auth F]	BA [auth E] CA [auth E] G [auth A] HA [auth F] IA [auth F] BA [auth E], CA [auth E], G [auth A], HA [auth F], IA [auth F], JA [auth F], L [auth B], Q [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain G [auth A] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain G [auth A] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	AA [auth D] FA [auth E] GA [auth E] I [auth A] J [auth A] AA [auth D], FA [auth E], GA [auth E], I [auth A], J [auth A], K [auth A], NA [auth F], O [auth B], OA [auth F], P [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.225 (Depositor), 0.231 (DCC)
R-Value Work: 0.180 (Depositor), 0.188 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.317	α = 90
b = 175.841	β = 90
c = 210.742	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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: 2006-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description