1XSI | pdb_00001xsi

Structure of a Family 31 alpha glycosidase

PDB DOI: https://doi.org/10.2210/pdb1XSI/pdb

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

Deposited: 2004-10-19 Released: 2004-10-26
Deposition Author(s): Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G., Strynadka, N.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.200 (Depositor), 0.208 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanistic and Structural Analysis of a Family 31 alpha-Glycosidase and Its Glycosyl-enzyme Intermediate

Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G., Strynadka, N.C.

(2005) J Biological Chem 280: 2105-2115

PubMed: 15501829 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M410468200
Primary Citation Related Structures:
1XSI, 1XSJ, 1XSK

PubMed Abstract:
We have determined the first structure of a family 31 alpha-glycosidase, that of YicI from Escherichia coli, both free and trapped as a 5-fluoroxylopyranosyl-enzyme intermediate via reaction with 5-fluoro-alpha-D-xylopyranosyl fluoride. Our 2.2-A resolution structure shows an intimately associated hexamer with structural elements from several monomers converging at each of the six active sites. Our kinetic and mass spectrometry analyses verified several of the features observed in our structural data, including a covalent linkage from the carboxylate side chain of the identified nucleophile Asp(416) to C-1 of the sugar ring. Structure-based sequence comparison of YicI with the mammalian alpha-glucosidases lysosomal alpha-glucosidase and sucrase-isomaltase predicts a high level of structural similarity and provides a foundation for understanding the various mutations of these enzymes that elicit human disease.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Macromolecule Content

Total Structure Weight: 536.76 kDa
Atom Count: 38,490
Modeled Residue Count: 4,638
Deposited Residue Count: 4,668
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	778	Escherichia coli	Mutation(s): 0 Gene Names: yicI EC: 3.2.1 (PDB Primary Data), 3.2.1.177 (UniProt)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPO Query on MPO Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B]	P [auth B], S [auth C], V [auth D], X [auth E]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] DA [auth F] G [auth A] AA [auth F], BA [auth F], CA [auth F], DA [auth F], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], W [auth E], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain J [auth A] SDF format, chain EA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth F]	EA [auth F], J [auth A], Y [auth E]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain J [auth A] Focus chain Y [auth E] Interactions & Density Focus chain EA [auth F] Focus chain J [auth A] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.239 (Depositor), 0.243 (DCC)
R-Value Work: 0.200 (Depositor), 0.208 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.686	α = 90
b = 174.926	β = 90
c = 209.509	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations