PDBsum entry 8std

Lyase

PDB id: 8std

Contents

Protein chains

203 a.a.

217 a.a.

Ligands

DND ×6

Metals

_MG ×9

PDB id:

8std

Name:

Lyase

Title:

S127a variant of larb, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate naad and soaked with cs2

Structure:

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase. Chain: a, b, c, d, e, f. Synonym: p2cmn synthase,lactate racemase accessory protein larb, lactate racemase activation protein larb,lactate racemase maturation protein larb,lactate racemization operon protein larb,nickel-pincer cofactor biosynthesis protein larb,nicotinic acid adenine dinucleotide carboxylase/hydrolase,naad carboxylase/hydrolase. Engineered: yes. Mutation: yes

Source:

Lactiplantibacillus plantarum wcfs1. Organism_taxid: 220668. Strain: atcc baa-793 / ncimb 8826 / wcfs1. Gene: larb, lp_0105. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.65Å R-factor: 0.243 R-free: 0.273

Authors:

S.Chatterjee,J.A.Rankin,J.Hu,R.P.Hausinger

Key ref:

S.Chatterjee et al. (2023). Structure of the larb-Substrate complex and identific of a reaction intermediate during nickel-Pincer nucle cofactor biosynthesis.. Biochemistry, 62, 3096. PubMed id: 37831946 DOI: 10.1021/ACS.BIOCHEM.3C00242

Date:

10-May-23 Release date: 27-Dec-23

Protein chains

F9UST0  (LARB_LACPL) -  Pyridinium-3,5-biscarboxylic acid mononucleotide synthase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

Seq: 246 a.a.

Struc: 203 a.a.*

Protein chain

F9UST0  (LARB_LACPL) -  Pyridinium-3,5-biscarboxylic acid mononucleotide synthase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

Seq: 246 a.a.

Struc: 217 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, F: E.C.2.5.1.143 - pyridinium-3,5-biscarboxylic acid mononucleotide synthase.
• Reaction: deamido-NAD⁺ + hydrogencarbonate = pyridinium-3,5-dicarboxylate mononucleotide + AMP + 2 H⁺

deamido-NAD(+) + hydrogencarbonate = pyridinium-3,5-dicarboxylate mononucleotide (Bound ligand (Het Group name = DND) matches with 52.27% similarity) + AMP + 2 × H(+)

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