5JAB | pdb_00005jab

Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420

PDB DOI: https://doi.org/10.2210/pdb5JAB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-04-12 Released: 2016-07-13
Deposition Author(s): Ahmed, F.H., Carr, P.D., Jackson, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.217 (Depositor), 0.226 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis.

Ahmed, F.H., Mohamed, A.E., Carr, P.D., Lee, B.M., Condic-Jurkic, K., O'Mara, M.L., Jackson, C.J.

(2016) Protein Sci 25: 1692-1709

PubMed: 27364382 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.2975
Primary Citation Related Structures:
5JAB

PubMed Abstract:
Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.

Organizational Affiliation

Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.

Macromolecule Content

Total Structure Weight: 63.02 kDa
Atom Count: 5,032
Modeled Residue Count: 523
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biliverdin reductase Rv2074	A, B, C, D	135	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv2074, MTCY49.13 EC: 1.3.98
UniProt
Find proteins for P9WLL7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WLL7 Go to UniProtKB: P9WLL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WLL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6J4 Query on 6J4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	COENZYME F420-3 C₃₄ H₄₃ N₆ O₂₁ P YHDAXCLOUDHUAA-LROHGRLLSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.217 (Depositor), 0.226 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.756	α = 90
b = 88.62	β = 90
c = 98.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Ahmed, F.H.

Carr, P.D.

Jackson, C.J.

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 1.1: 2016-08-31
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Data collection, Database references, Derived calculations
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description