3QJ4

Crystal structure of Human Renalase (isoform 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

FAD-binding site and NADP reactivity in human renalase: a new enzyme involved in blood pressure regulation

Milani, M.Ciriello, F.Baroni, S.Pandini, V.Canevari, G.Bolognesi, M.Aliverti, A.

(2011) J.Mol.Biol. 411: 463-473

  • DOI: 10.1016/j.jmb.2011.06.010

  • PubMed Abstract: 
  • Renalase is a recently discovered flavoprotein that regulates blood pressure, regulates sodium and phosphate excretion, and displays cardioprotectant action through a mechanism that is barely understood to date. It has been proposed to act as a catec ...

    Renalase is a recently discovered flavoprotein that regulates blood pressure, regulates sodium and phosphate excretion, and displays cardioprotectant action through a mechanism that is barely understood to date. It has been proposed to act as a catecholamine-degrading enzyme, via either O(2)-dependent or NADH-dependent mechanisms. Here we report the renalase crystal structure at 2.5 Å resolution together with new data on its interaction with nicotinamide dinucleotides. Renalase adopts the p-hydroxybenzoate hydroxylase fold topology, comprising a Rossmann-fold-based flavin adenine dinucleotide (FAD)-binding domain and a putative substrate-binding domain, the latter of which contains a five-stranded anti-parallel β-sheet. A large cavity (228 Å(3)), facing the flavin ring, presumably represents the active site. Compared to monoamine oxidase or polyamine oxidase, the renalase active site is fully solvent exposed and lacks an 'aromatic cage' for binding the substrate amino group. Renalase has an extremely low diaphorase activity, displaying lower k(cat) but higher k(cat)/K(m) for NADH compared to NADPH. Moreover, its FAD prosthetic group becomes slowly reduced when it is incubated with NADPH under anaerobiosis, and binds NAD(+) or NADP(+) with K(d) values of ca 2 mM. The absence of a recognizable NADP-binding site in the protein structure and its poor affinity for, and poor reactivity towards, NADH and NADPH suggest that these are not physiological ligands of renalase. Although our study does not answer the question on the catalytic activity of renalase, it provides a firm framework for testing hypotheses on the molecular mechanism of its action.


    Organizational Affiliation

    Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Renalase
A, B
342Homo sapiensMutation(s): 0 
Gene Names: RNLS (C10orf59)
EC: 1.6.3.5
Find proteins for Q5VYX0 (Homo sapiens)
Go to Gene View: RNLS
Go to UniProtKB:  Q5VYX0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.837α = 90.00
b = 86.593β = 95.30
c = 93.180γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references