4UDG | pdb_00004udg

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate

PDB DOI: https://doi.org/10.2210/pdb4UDG/pdb

Classification: TRANSFERASE
Organism(s): uncultured organism
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-12-10 Released: 2015-05-27
Deposition Author(s): Ladeveze, S., Cioci, G., Potocki-Veronese, G., Tranier, S., Mourey, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.183 (Depositor), 0.194 (DCC)
R-Value Work:
0.154 (Depositor), 0.168 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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Literature

Structural Bases for N-Glycan Processing by Mannoside Phosphorylase.

Ladeveze, S., Cioci, G., Roblin, P., Mourey, L., Tranier, S., Potocki-Veronese, G.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1335

PubMed: 26057673 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1399004715006604
Primary Citation Related Structures:
4UDG, 4UDI, 4UDJ, 4UDK

PubMed Abstract:
The first crystal structure of Uhgb_MP, a β-1,4-mannopyranosyl-chitobiose phosphorylase belonging to the GH130 family which is involved in N-glycan degradation by human gut bacteria, was solved at 1.85 Å resolution in the apo form and in complex with mannose and N-acetylglucosamine. SAXS and crystal structure analysis revealed a hexameric structure, a specific feature of GH130 enzymes among other glycoside phosphorylases. Mapping of the -1 and +1 subsites in the presence of phosphate confirmed the conserved Asp104 as the general acid/base catalytic residue, which is in agreement with a single-step reaction mechanism involving Man O3 assistance for proton transfer. Analysis of this structure, the first to be solved for a member of the GH130_2 subfamily, revealed Met67, Phe203 and the Gly121-Pro125 loop as the main determinants of the specificity of Uhgb_MP and its homologues towards the N-glycan core oligosaccharides and mannan, and the molecular bases of the key role played by GH130 enzymes in the catabolism of dietary fibre and host glycans.

Organizational Affiliation

Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France.

Macromolecule Content

Total Structure Weight: 239.02 kDa
Atom Count: 17,360
Modeled Residue Count: 1,922
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UHGB_MP	A, B, C, D, E A, B, C, D, E, F	347	uncultured organism	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for D9ZDQ9 (uncultured organism) Explore D9ZDQ9 Go to UniProtKB: D9ZDQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9ZDQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	AA [auth E] GA [auth F] H [auth A] N [auth B] S [auth C] AA [auth E], GA [auth F], H [auth A], N [auth B], S [auth C], W [auth D]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain AA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	FA [auth F] G [auth A] M [auth B] R [auth C] V [auth D] FA [auth F], G [auth A], M [auth B], R [auth C], V [auth D], Z [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FA [auth F] Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain FA [auth F] Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	BA [auth E] HA [auth F] I [auth A] O [auth B] P [auth B] BA [auth E], HA [auth F], I [auth A], O [auth B], P [auth B], T [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	DA [auth E], EA [auth E], JA [auth F], K [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	CA [auth E] IA [auth F] J [auth A] Q [auth B] U [auth C] CA [auth E], IA [auth F], J [auth A], Q [auth B], U [auth C], Y [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.183 (Depositor), 0.194 (DCC)
R-Value Work: 0.154 (Depositor), 0.168 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.816	α = 90
b = 140.912	β = 90
c = 168.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2015-06-17
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary