7FIS

The crystal structure of beta-1,2-mannobiose phosphorylase in complex with mannose 1-phosphate (M1P)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural investigation of a thermostable 1,2-beta-mannobiose phosphorylase from Thermoanaerobacter sp. X-514.

Dai, L.Chang, Z.Yang, J.Liu, W.Yang, Y.Chen, C.C.Zhang, L.Huang, J.W.Sun, Y.Guo, R.T.

(2021) Biochem Biophys Res Commun 579: 54-61

  • DOI: 10.1016/j.bbrc.2021.09.046
  • Primary Citation of Related Structures:  
    7FIP, 7FIQ, 7FIR, 7FIS

  • PubMed Abstract: 
  • 1,2-β-Mannobiose phosphorylases (1,2-β-MBPs) from glycoside hydrolase 130 (GH130) family are important bio-catalysts in glycochemistry applications owing to their ability in synthesizing oligomannans. Here, we report the crystal structure of a thermostable 1,2-β-MBP from Thermoanaerobacter sp ...

    1,2-β-Mannobiose phosphorylases (1,2-β-MBPs) from glycoside hydrolase 130 (GH130) family are important bio-catalysts in glycochemistry applications owing to their ability in synthesizing oligomannans. Here, we report the crystal structure of a thermostable 1,2-β-MBP from Thermoanaerobacter sp. X-514 termed Teth514_1789 to reveal the molecular basis of its higher thermostability and mechanism of action. We also solved the enzyme complexes of mannose, mannose-1-phosphate (M1P) and 1,4-β-mannobiose to manifest the enzyme-substrate interaction networks of three main subsites. Notably, a Zn ion that should be derived from crystallization buffer was found in the active site and coordinates the phosphate moiety of M1P. Nonetheless, this Zn-coordination should reflect an inhibitory status as supplementing Zn severely impairs the enzyme activity. These results indicate that the effects of metal ions should be taken into consideration when applying Teth514_1789 and other related enzymes. Based on the structure, a reliable model of Teth514_1788 that shares 61.7% sequence identity to Teth514_1789 but displays a different substrate preference was built. Analyzing the structural features of these two closely related enzymes, we hypothesized that the length of a loop fragment that covers the entrance of the catalytic center might regulate the substrate selectivity. In conclusion, these information provide in-depth understanding of GH130 1,2-β-MBPs and should serve as an important guidance for enzyme engineering for further applications.


    Organizational Affiliation

    National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China. Electronic address: guoreyting@hubu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-1,2-mannobiose phosphorylaseC [auth A],
B,
A [auth C],
D
313Thermoanaerobacter sp. X514Mutation(s): 0 
Gene Names: Teth514_1789
EC: 2.4.1.339
UniProt
Find proteins for B0K2C3 (Thermoanaerobacter sp. (strain X514))
Explore B0K2C3 
Go to UniProtKB:  B0K2C3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0K2C3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M1P (Subject of Investigation/LOI)
Query on M1P

Download Ideal Coordinates CCD File 
E [auth C],
K [auth B],
M [auth B],
S [auth A],
Y [auth D]
1-O-phosphono-alpha-D-mannopyranose
C6 H13 O9 P
HXXFSFRBOHSIMQ-RWOPYEJCSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
Z [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth C],
L [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
DA [auth D],
G [auth C],
H [auth C],
BA [auth D],
CA [auth D],
DA [auth D],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.959α = 90
b = 204.959β = 90
c = 78.482γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2021YFC2100300

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references, Source and taxonomy, Structure summary