PDBsum entry 5ls7

Lyase

PDB id: 5ls7

Contents

Protein chains

25 a.a.

128 a.a.

102 a.a.

Ligands

GOL ×2

PEG ×2

ACO

CO2 ×3

SCN ×2

74C

Metals

_MG

Waters ×294

PDB id:

5ls7

Name:

Lyase

Title:

Complex of wild type e. Coli alpha aspartate decarboxylase with its processing factor panz

Structure:

Aspartate 1-decarboxylase. Chain: a. Synonym: aspartate alpha-decarboxylase. Engineered: yes. Other_details: residues 1-17 are the purification tag.. Pand maturation factor. Chain: b. Engineered: yes. Other_details: thE C-terminus is not visible in the electron density.

Source:

Escherichia coli k-12. Organism_taxid: 83333. Gene: pand, b0131, jw0127. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: panm, panz, yhhk, b3459, jw3424. Expression_system_taxid: 562

Resolution:

1.16Å R-factor: 0.115 R-free: 0.137

Authors:

D.C.F.Monteiro,M.E.Webb,A.R.Pearson

Key ref:

Z.L.P.Arnott et al. (2017). The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ·AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Biochemistry, 56, 4931-4939. PubMed id: 28832133

Date:

22-Aug-16 Release date: 13-Sep-17

Protein chain

P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase from Escherichia coli (strain K12)

Seq: 126 a.a.

Struc: 25 a.a.

Protein chain

P37613  (PANZ_ECOLI) -  PanD regulatory factor from Escherichia coli (strain K12)

Seq: 127 a.a.

Struc: 128 a.a.

Protein chain

P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase from Escherichia coli (strain K12)

Seq: 126 a.a.

Struc: 102 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, D: E.C.4.1.1.11 - aspartate 1-decarboxylase.
• Pathway: Coenzyme A Biosynthesis (early stages)
• Reaction: L-aspartate + H⁺ = beta-alanine + CO2

L-aspartate + H(+) = beta-alanine (Bound ligand (Het Group name = GOL) matches with 71.43% similarity) + CO2 (Bound ligand (Het Group name = CO2) corresponds exactly)

• Cofactor: Pyruvate
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

Biochemistry 56:4931-4939 (2017)

PubMed id: 28832133

The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ·AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan).

Z.L.P.Arnott, S.Nozaki, D.C.F.Monteiro, H.E.Morgan, A.R.Pearson, H.Niki, M.E.Webb.

ABSTRACT

The antimetabolite pentyl pantothenamide has broad spectrum antibiotic activity but exhibits enhanced activity against Escherichia coli. The PanDZ complex has been proposed to regulate the pantothenate biosynthetic pathway in E. coli by limiting the supply of β-alanine in response to coenzyme A concentration. We show that formation of such a complex between activated aspartate decarboxylase (PanD) and PanZ leads to sequestration of the pyruvoyl cofactor as a ketone hydrate and demonstrate that both PanZ overexpression-linked β-alanine auxotrophy and pentyl pantothenamide toxicity are due to formation of this complex. This both demonstrates that the PanDZ complex regulates pantothenate biosynthesis in a cellular context and validates the complex as a target for antibiotic development.