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

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1107/S1399004715006604
  • Primary Citation of 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
347uncultured organismMutation(s): 0 
EC: 2.4.1
Find proteins for D9ZDQ9 (uncultured organism)
Explore D9ZDQ9 
Go to UniProtKB:  D9ZDQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9ZDQ9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BMA

Download Ideal Coordinates CCD File 
DA [auth D]
H [auth A]
KA [auth E]
PA [auth F]
R [auth B]
DA [auth D],
H [auth A],
KA [auth E],
PA [auth F],
R [auth B],
Y [auth C]
C6 H12 O6
Query on PGE

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AA [auth C]
HA [auth D]
L [auth A]
M [auth A]
P [auth A]
AA [auth C],
HA [auth D],
L [auth A],
M [auth A],
P [auth A],
T [auth B],
TA [auth F],
V [auth B],
W [auth B]
C6 H14 O4
Query on PO4

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CA [auth D]
G [auth A]
JA [auth E]
OA [auth F]
Q [auth B]
CA [auth D],
G [auth A],
JA [auth E],
OA [auth F],
Q [auth B],
X [auth C]
O4 P
Query on EDO

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BA [auth C]
FA [auth D]
GA [auth D]
IA [auth D]
J [auth A]
BA [auth C],
FA [auth D],
GA [auth D],
IA [auth D],
J [auth A],
K [auth A],
MA [auth E],
NA [auth E],
RA [auth F],
SA [auth F],
U [auth B]
C2 H6 O2
Query on K

Download Ideal Coordinates CCD File 
EA [auth D]
I [auth A]
LA [auth E]
N [auth A]
O [auth A]
EA [auth D],
I [auth A],
LA [auth E],
N [auth A],
O [auth A],
QA [auth F],
S [auth B],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.88α = 90
b = 140.84β = 90
c = 168.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary