5AEE | pdb_00005aee

A bacterial protein structure in glycoside hydrolase family 31

PDB DOI: https://doi.org/10.2210/pdb5AEE/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-08-28 Released: 2016-02-10
Deposition Author(s): Jin, Y., Speciale, G., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.201 (Depositor), 0.205 (DCC)
R-Value Work:
0.163 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Yihq is a Sulfoquinovosidase that Cleaves Sulfoquinovosyl Diacylglyceride Sulfolipids.

Speciale, G., Jin, Y., Davies, G.J., Williams, S.J., Goddard-Borger, E.D.

(2016) Nat Chem Biol 12: 215

PubMed: 26878550 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.2023
Primary Citation Related Structures:
5AED, 5AEE, 5AEG

PubMed Abstract:
Sulfoquinovose is produced by photosynthetic organisms at a rate of 10(10) tons per annum and is degraded by bacteria as a source of carbon and sulfur. We have identified Escherichia coli YihQ as the first dedicated sulfoquinovosidase and the gateway enzyme to sulfoglycolytic pathways. Structural and mutagenesis studies unveiled the sequence signatures for binding the distinguishing sulfonate residue and revealed that sulfoquinovoside degradation is widespread across the tree of life.

Organizational Affiliation

School of Chemistry, University of Melbourne, Parkville, Victoria, Australia.

Macromolecule Content

Total Structure Weight: 157.85 kDa
Atom Count: 11,403
Modeled Residue Count: 1,335
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCOSIDASE YIHQ	A, B	686	Escherichia coli K-12	Mutation(s): 1 EC: 3.2.1.20 (PDB Primary Data), 3.2.1.199 (UniProt)
UniProt
Find proteins for P32138 (Escherichia coli (strain K12)) Explore P32138 Go to UniProtKB: P32138
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32138
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NSQ Query on NSQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	4-nitrophenyl alpha-D-6-sulfoquinovoside C₁₂ H₁₅ N O₁₀ S JRVQBBIDMNDOQV-ZIQFBCGOSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	C [auth A], D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.201 (Depositor), 0.205 (DCC)
R-Value Work: 0.163 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.96	α = 90
b = 107.62	β = 107.85
c = 103.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2016-03-02
Changes: Database references
Version 1.2: 2016-03-30
Changes: Database references
Version 1.3: 2019-05-22
Changes: Data collection, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary