1UP6 | pdb_00001up6

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb1UP6/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-09-29 Released: 2004-08-02
Deposition Author(s): Varrot, A., Yip, V.L., Withers, S.G., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.250 (Depositor), 0.296 (DCC)
R-Value Work:
0.200 (Depositor), 0.264 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 Beta-Glycosidase from Thermotoga Maritima.

Yip, V.L., Varrot, A., Davies, G.J., Rajan, S.S., Yang, X., Thompson, J., Anderson, W.F., Withers, S.G.

(2004) J Am Chem Soc 126: 8354

PubMed: 15237973 Search on PubMed
DOI: https://doi.org/10.1021/ja047632w
Primary Citation Related Structures:
1UP6

PubMed Abstract:
Among the numerous well-characterized families of glycosidases, family 4 appears to be the anomaly, requiring both catalytic NAD+ and a divalent metal for activity. The unusual cofactor requirement prompted the proposal of a mechanism involving key NAD+-mediated redox steps as well as elimination of the glycosidic oxygen. Primary kinetic isotope effects for the 2- and 3-deutero substrate analogues, isotopic exchange with solvent, and structural analysis of a 6-phospho-beta-glucosidase, BglT (E.C. 3.2.1.6), provided evidence in support of the proposed mechanism, which has striking resemblances to that of the sugar dehydratases. Furthermore, analysis of the stereochemical outcome indicated that family 4 enzymes are retaining glycosidases.

Organizational Affiliation

Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1.

Macromolecule Content

Total Structure Weight: 388.45 kDa
Atom Count: 26,917
Modeled Residue Count: 3,222
Deposited Residue Count: 3,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHO-BETA-GLUCOSIDASE	A, B, C, D, E A, B, C, D, E, F, G, H	416	Thermotoga maritima MSB8	Mutation(s): 0 EC: 3.2.1.6 (PDB Primary Data), 3.2.1.86 (UniProt)
UniProt
Find proteins for Q9X108 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X108 Go to UniProtKB: Q9X108
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X108
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain T [auth G] SDF format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth G] MOL2 format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth G] mmCIF format, chain I [auth A]	I [auth A], O [auth C], T [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain T [auth G] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain T [auth G]
G6P Query on G6P Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C]	K [auth A], Q [auth C]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth C] Interactions & Density Focus chain K [auth A] Focus chain Q [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain V [auth G] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth G] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth G]	N [auth B], R [auth D], S [auth E], V [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth E] Focus chain V [auth G] Interactions & Density Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth E] Focus chain V [auth G]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth C] SDF format, chain U [auth G] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth G] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth G]	J [auth A], L [auth A], M [auth A], P [auth C], U [auth G]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain U [auth G] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain U [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.250 (Depositor), 0.296 (DCC)
R-Value Work: 0.200 (Depositor), 0.264 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.438	α = 90
b = 179.438	β = 90
c = 282.911	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-08-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-08-02
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-10-09
Changes: Structure summary