PfkB(Mycobacterium marinum)

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7FCA


Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum.

Gao, B.Ji, R.Li, Z.Su, X.Li, H.Sun, Y.Ji, C.Gan, J.Li, J.

(2021) Biochem Biophys Res Commun 579: 129-135

  • DOI: https://doi.org/10.1016/j.bbrc.2021.09.051
  • Primary Citation of Related Structures:  
    7CF8, 7FCA

  • PubMed Abstract: 

    Phosphofructokinase B (PfkB) belongs to the ribokinase family, which uses the phosphorylated sugar as substrate, and catalyzes fructose-6-phosphate into fructose-1,6-diphosphate. However, the structural basis of Mycobacterium marinum PfkB is not clear. Here, we found that the PfkB protein was monomeric in solution, which was different from most enzymes in this family. The crystal structure of PfkB protein from M. marinum was solved at a resolution of 2.21 Å. The PfkB structure consists of two domains, a major three-layered α/β/α sandwich-like domain characteristic of the ribokinase-like superfamily, and a second domain composed of four-stranded β sheets. Structural comparison analysis suggested that residues G236, A237, G238, and D239 could be critical for ATP catalysis and substrate binding of PfkB. Our current work provides new insights into understanding the mechanism of the glycolysis in M. marinum.

  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructokinase, PfkB
A, B, C, D, E
A, B, C, D, E, F
303Mycobacterium marinum MMutation(s): 0 
Gene Names: pfkBMMAR_4574
Find proteins for B2HEF4 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Explore B2HEF4 
Go to UniProtKB:  B2HEF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2HEF4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.415α = 90
b = 125.406β = 106.834
c = 137.518γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500600

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description