7KPZ

1.70 A resolution crystal structure of Group A Streptococcus HupZ-V5-His6

  • Classification: OXIDOREDUCTASE
  • Organism(s): Streptococcus sp.
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-11-13 Released: 2021-02-10 
  • Deposition Author(s): Li, J., Liu, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Heme Binding to HupZ with a C-Terminal Tag from Group A Streptococcus.

Traore, E.S.Li, J.Chiura, T.Geng, J.Sachla, A.J.Yoshimoto, F.Eichenbaum, Z.Davis, I.Mak, P.J.Liu, A.

(2021) Molecules 26

  • DOI: https://doi.org/10.3390/molecules26030549
  • Primary Citation of Related Structures:  
    7KPZ, 7KQ2

  • PubMed Abstract: 

    HupZ is an expected heme degrading enzyme in the heme acquisition and utilization pathway in Group A Streptococcus. The isolated HupZ protein containing a C-terminal V5-His 6 tag exhibits a weak heme degradation activity. Here, we revisited and characterized the HupZ-V5-His 6 protein via biochemical, mutagenesis, protein quaternary structure, UV-vis, EPR, and resonance Raman spectroscopies. The results show that the ferric heme-protein complex did not display an expected ferric EPR signal and that heme binding to HupZ triggered the formation of higher oligomeric states. We found that heme binding to HupZ was an O 2 -dependent process. The single histidine residue in the HupZ sequence, His111, did not bind to the ferric heme, nor was it involved with the weak heme-degradation activity. Our results do not favor the heme oxygenase assignment because of the slow binding of heme and the newly discovered association of the weak heme degradation activity with the His 6 -tag. Altogether, the data suggest that the protein binds heme by its His 6 -tag, resulting in a heme-induced higher-order oligomeric structure and heme stacking. This work emphasizes the importance of considering exogenous tags when interpreting experimental observations during the study of heme utilization proteins.


  • Organizational Affiliation

    Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HupZ
A, B
165Streptococcus sp.Mutation(s): 0 
Gene Names: MGAS10270_Spy0711
EC: 1.4.3.5
UniProt
Find proteins for Q9A0B9 (Streptococcus pyogenes serotype M1)
Explore Q9A0B9 
Go to UniProtKB:  Q9A0B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A0B9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.02α = 90
b = 62.378β = 90
c = 94.884γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2021-02-10 
  • Deposition Author(s): Li, J., Liu, A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01CA247379
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description