6PLE

Crystal structure of MhuD R26S mutant in complex with biliverdin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of aMycobacterium tuberculosisHeme-Degrading Protein, MhuD, Variant in Complex with Its Product.

Chao, A.Burley, K.H.Sieminski, P.J.de Miranda, R.Chen, X.Mobley, D.L.Goulding, C.W.

(2019) Biochemistry 58: 4610-4620

  • DOI: 10.1021/acs.biochem.9b00726
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, requires iron for survival. In Mtb, MhuD is the cytosolic protein that degrades imported heme. MhuD is distinct, in both sequence and structure, from canonical heme oxyge ...

    Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, requires iron for survival. In Mtb, MhuD is the cytosolic protein that degrades imported heme. MhuD is distinct, in both sequence and structure, from canonical heme oxygenases (HOs) but homologous with IsdG-type proteins. Canonical HO is found mainly in eukaryotes, while IsdG-type proteins are predominantly found in prokaryotes, including pathogens. While there are several published structures of MhuD and other IsdG-type proteins in complex with the heme substrate, no structures of IsdG-type proteins in complex with a product have been reported, unlike the case for HOs. We recently showed that the Mtb variant MhuD-R26S produces biliverdin IXα (αBV) rather than the wild-type mycobilin isomers. Given that mycobilin and other IsdG-type protein products like staphylobilin are difficult to isolate in quantities sufficient for structure determination, here we use the MhuD-R26S variant and its product αBV as a proxy to study the IsdG-type protein-product complex. First, we show that αBV has a nanomolar affinity for MhuD and the R26S variant. Second, we determined the MhuD-R26S-αBV complex structure to 2.5 Å, which reveals two notable features: (1) two αBV molecules bound per active site and (2) a novel α-helix (α3) that was not observed in previous MhuD-heme structures. Finally, through molecular dynamics simulations, we show that α3 is stable with the proximal αBV alone. MhuD's high affinity for the product and the observed structural and electrostatic changes that accompany substrate turnover suggest that there may be an unidentified class of proteins that are responsible for the extraction of products from MhuD and other IsdG-type proteins.


    Organizational Affiliation

    Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme oxygenase (mycobilin-producing)A, B123Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: mhuDRv3592
EC: 1.14.99.57
Find proteins for P9WKH3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKH3 
Go to UniProtKB:  P9WKH3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download CCD File 
A, B
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.237 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.22α = 90
b = 113.61β = 90
c = 113.65γ = 90
Software Package:
Software NamePurpose
BOSdata collection
pointlessdata scaling
MOSFLMdata reduction
PHENIXphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1321846
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI095208

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Database references