PDBsum entry 5udw

Transferase

PDB id: 5udw

Contents

Protein chains

253 a.a.

240 a.a.

Ligands

PO4 ×6

SO4 ×14

Metals

_NI ×11

Waters ×98

PDB id:

5udw

Name:

Transferase

Title:

Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with nickel

Structure:

Lactate racemization operon protein lare. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Lactobacillus plantarum (strain atcc baa-793 / ncimb 8826 / wcfs1). Organism_taxid: 220668. Strain: atcc baa-793 / ncimb 8826 / wcfs1. Gene: lare, lp_0109. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.201 R-free: 0.257

Authors:

M.Fellner,B.Desguin,R.P.Hausinger,J.Hu

Key ref:

M.Fellner et al. (2017). Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc Natl Acad Sci U S A, 114, 9074-9079. PubMed id: 28784764

Date:

28-Dec-16 Release date: 23-Aug-17

Protein chains

F9UST4  (LARE_LACPL) -  Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

Seq: 276 a.a.

Struc: 253 a.a.

Protein chains

F9UST4  (LARE_LACPL) -  Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

Seq: 276 a.a.

Struc: 240 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F: E.C.4.4.1.37 - intrinsic cysteine-dependent pyridinium-3,5-bisthiocarboxylic acid
• Reaction:
  1. pyridinium-3,5-dicarboxylate mononucleotide + [LarE protein]-L- cysteine + ATP = [LarE protein]-dehydroalanine + pyridinium-3- carboxylate-5-thiocarboxylate mononucleotide + AMP + diphosphate + H⁺
  2. [LarE protein]-L-cysteine + pyridinium-3-carboxylate-5- thiocarboxylate mononucleotide + ATP = pyridinium-3,5-bisthiocarboxylate mononucleotide + [LarE protein]-dehydroalanine + AMP + diphosphate + H⁺

pyridinium-3,5-dicarboxylate mononucleotide + [LarE protein]-L- cysteine + ATP = [LarE protein]-dehydroalanine + pyridinium-3- carboxylate-5-thiocarboxylate mononucleotide + AMP (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate + H(+)

[LarE protein]-L-cysteine + pyridinium-3-carboxylate-5- thiocarboxylate mononucleotide + ATP = pyridinium-3,5-bisthiocarboxylate mononucleotide + [LarE protein]-dehydroalanine + AMP (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate + H(+)

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

reference

Proc Natl Acad Sci U S A 114:9074-9079 (2017)

PubMed id: 28784764

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.

M.Fellner, B.Desguin, R.P.Hausinger, J.Hu.

ABSTRACT

Thelaroperon inLactobacillus plantarumencodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.