PDBsum entry 4zcc

Oxidoreductase

PDB id: 4zcc

Contents

Protein chains

320 a.a.

Ligands

FAD ×4

NAI ×4

FMT ×4

Waters ×736

PDB id:

4zcc

Name:

Oxidoreductase

Title:

Renalase in complex with nadh

Structure:

Renalase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Pseudomonas syringae pv. Phaseolicola (strain 1448a / race 6). Organism_taxid: 264730. Strain: 1448a / race 6. Variant: race 6. Gene: pspph_1014. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.171 R-free: 0.215

Authors:

N.R.Silvaggi,G.R.Moran,J.V.Roman

Key ref:

M.R.Hoag et al. (2015). Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-β-NAD(P) Oxidase Activity from Pseudomonas phaseolicola. Biochemistry, 54, 3791-3802. PubMed id: 26016690 DOI: 10.1021/acs.biochem.5b00451

Date:

15-Apr-15 Release date: 15-Jul-15

Protein chains

Q48MT7  (RNLS_PSE14) -  Renalase from Pseudomonas savastanoi pv. phaseolicola (strain 1448A / Race 6)

Seq: 328 a.a.

Struc: 320 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.6.3.5 - renalase.
• Reaction:
  1. 1,2-dihydro-beta-NAD + O2 + H⁺ = H2O2 + NAD⁺
  2. 1,2-dihydro-beta-NADP + O2 + H⁺ = H2O2 + NADP⁺
  3. 1,6-dihydro-beta-NAD + O2 + H⁺ = H2O2 + NAD⁺
  4. 1,6-dihydro-beta-NADP + O2 + H⁺ = H2O2 + NADP⁺

1,2-dihydro-beta-NAD + O2 + H(+) = H2O2 + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly)

1,2-dihydro-beta-NADP + O2 + H(+) = H2O2 + NADP(+) (Bound ligand (Het Group name = NAI) matches with 91.67% similarity)

1,6-dihydro-beta-NAD + O2 + H(+) = H2O2 + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly)

1,6-dihydro-beta-NADP + O2 + H(+) = H2O2 + NADP(+) (Bound ligand (Het Group name = NAI) matches with 91.67% similarity)

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acs.biochem.5b00451

Biochemistry 54:3791-3802 (2015)

PubMed id: 26016690

Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-β-NAD(P) Oxidase Activity from Pseudomonas phaseolicola.

M.R.Hoag, J.Roman, B.A.Beaupre, N.R.Silvaggi, G.R.Moran.

ABSTRACT

Despite a lack of convincing in vitro evidence and a number of sound refutations, it is widely accepted that renalase is an enzyme unique to animals that catalyzes the oxidative degradation of catecholamines in blood in order to lower vascular tone. Very recently, we identified isomers of β-NAD(P)H as substrates for renalase (Beaupre, B. A. et al. (2015) Biochemistry, 54, 795-806). These molecules carry the hydride equivalent on the 2 or 6 position of the nicotinamide base and presumably arise in nonspecific redox reactions of nicotinamide dinucleotides. Renalase serves to rapidly oxidize these isomers to form β-NAD(P)(+) and then pass the electrons to dioxygen, forming H2O2. We have also shown that these substrate molecules are highly inhibitory to dehydrogenase enzymes and thus have proposed an intracellular metabolic role for this enzyme. Here, we identify a renalase from an organism without a circulatory system. This bacterial form of renalase has the same substrate specificity profile as that of human renalase but, in terms of binding constant (Kd), shows a marked preference for substrates derived from β-NAD(+). 2-dihydroNAD(P) substrates reduce the enzyme with rate constants (kred) that greatly exceed those for 6-dihydroNAD(P) substrates. Taken together, kred/Kd values indicate a minimum 20-fold preference for 2DHNAD. We also offer the first structures of a renalase in complex with catalytically relevant ligands β-NAD(+) and β-NADH (the latter being an analogue of the substrate(s)). These structures show potential electrostatic repulsion interactions with the product and a unique binding orientation for the substrate nicotinamide base that is consistent with the identified activity.