Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.55 kDa 
• Atom Count: 9216 
• Modelled Residue Count: 906 
• Deposited Residue Count: 912 
• Unique protein chains: 1

1LQT

A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase

• DOI: 10.2210/pdb1LQT/pdb

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


• Deposited: 2002-05-13 Released: 2002-07-31 
• Deposition Author(s): Bossi, R.T., Aliverti, A., Raimondi, D., Fischer, F., Zanetti, G., Ferrari, D., Tahallah, N., Maier, C.S., Heck, A.J.R., Rizzi, M., Mattevi, A., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 

Literature

A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase.

Bossi, R.T., Aliverti, A., Raimondi, D., Fischer, F., Zanetti, G., Ferrari, D., Tahallah, N., Maier, C.S., Heck, A.J.R., Rizzi, M., Mattevi, A.

(2002) Biochemistry 41: 8807-8818

• PubMed: 12102623 
• DOI: 10.1021/bi025858a
• Primary Citation of Related Structures:  
  1LQU, 1LQT


• PubMed Abstract: 
  

FprA is a mycobacterial oxidoreductase that catalyzes the transfer of reducing equivalents from NADPH to a protein acceptor. We determined the atomic resolution structure of FprA in the oxidized (1.05 A resolution) and NADPH-reduced (1.25 A resolution) forms. The comparison of these FprA structures with that of bovine adrenodoxin reductase showed no significant overall differences. Hence, these enzymes, which belong to the structural family of the disulfide oxidoreductases, are structurally conserved in very distant organisms such as mycobacteria and mammals. Despite the conservation of the overall fold, the details of the active site of FprA show some peculiar features. In the oxidized enzyme complex, the bound NADP+ exhibits a covalent modification, which has been identified as an oxygen atom linked through a carbonylic bond to the reactive C4 atom of the nicotinamide ring. Mass spectrometry has confirmed this assignment. This NADP+ derivative is likely to form by oxidation of the NADP+ adduct resulting from nucleophilic attack by an active-site water molecule. A Glu-His pair is well positioned to activate the attacking water through a mechanism analogous to that of the catalytic triad in serine proteases. The NADP+ nicotinamide ring exhibits the unusual cis conformation, which may favor derivative formation. The physiological significance of this reaction is presently unknown. However, it could assist with drug-design studies in that the modified NADP+ could serve as a lead compound for the development of specific inhibitors.

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Organizational Affiliation: 

Dipartimento di Genetica e Microbiologia, Università di Pavia, via Abbiategrasso 207, 27100 Pavia, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FprA	A, B	456	Mycobacterium tuberculosis	Mutation(s): 0  EC: 1.18.1.2
UniProt
Find proteins for P9WIQ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIQ3  Go to UniProtKB:  P9WIQ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A], P [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ODP	I [auth A], Q [auth B]	4-OXO-NICOTINAMIDE-ADENINE DINUCLEOTIDE PHOSPHATE C21 H29 N7 O18 P3 PIXSDSMVQQICPA-BYJCYCELSA-O
ACT	C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.335	α = 90
b = 89.215	β = 90
c = 160.873	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BEAST	model building
REFMAC	refinement
CCP4	data scaling
BEAST	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-13 
• Released Date: 2002-07-31 
Deposition Author(s): Bossi, R.T., Aliverti, A., Raimondi, D., Fischer, F., Zanetti, G., Ferrari, D., Tahallah, N., Maier, C.S., Heck, A.J.R., Rizzi, M., Mattevi, A., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2002-07-31
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description