7VT9

CRYSTAL STRUCTURE AT 3.4 ANGSTROMS RESOLUTION OF Maltodextrin glucosidase, MalZ, FROM Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Dimeric architecture of maltodextrin glucosidase (MalZ) provides insights into the substrate recognition and hydrolysis mechanism.

Ahn, W.C.An, Y.Song, K.M.Park, K.H.Lee, S.J.Oh, B.H.Park, J.T.Woo, E.J.

(2022) Biochem Biophys Res Commun 586: 49-54

  • DOI: 10.1016/j.bbrc.2021.11.070
  • Primary Citation of Related Structures:  
    7VT9

  • PubMed Abstract: 
  • Maltodextrin glucosidase (MalZ) is a key enzyme in the maltose utilization pathway in Escherichia coli that liberates glucose from the reducing end of the short malto-oligosaccharides. Unlike other enzymes in the GH13_21 subfamily, the hydrolytic activity of MalZ is limited to maltodextrin rather than long starch substrates, forming various transglycosylation products in α-1,3, α-1,4 or α-1,6 linkages ...

    Maltodextrin glucosidase (MalZ) is a key enzyme in the maltose utilization pathway in Escherichia coli that liberates glucose from the reducing end of the short malto-oligosaccharides. Unlike other enzymes in the GH13_21 subfamily, the hydrolytic activity of MalZ is limited to maltodextrin rather than long starch substrates, forming various transglycosylation products in α-1,3, α-1,4 or α-1,6 linkages. The mechanism for the substrate binding and hydrolysis of this enzyme is not well understood yet. Here, we present the dimeric crystal structure of MalZ, with the N-domain generating a unique substrate binding groove. The N-domain bears CBM34 architecture and forms a part of the active site in the catalytic domain of the adjacent molecule. The groove found between the N-domain and catalytic domain from the adjacent molecule, shapes active sites suitable for short malto-oligosaccharides, but hinders long stretches of oligosaccharides. The conserved residue of E44 protrudes at subsite +2, elucidating the hydrolysis pattern of the substrate by the glucose unit from the reducing end. The structural analysis provides a molecular basis for the substrate specificity and the enzymatic property, and has potential industrial application for protein engineering.


    Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea; University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: ejwoo@kribb.re.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin glucosidaseA, B615Escherichia coli K-12Mutation(s): 0 
Gene Names: malZb0403JW0393
EC: 3.2.1.20
UniProt
Find proteins for P21517 (Escherichia coli (strain K12))
Explore P21517 
Go to UniProtKB:  P21517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21517
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.186α = 90
b = 204.186β = 90
c = 267.916γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021M3A9G8025599
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1A2C2011328

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release