5LS7

Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ

PDB DOI: https://doi.org/10.2210/pdb5LS7/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-22 Released: 2017-09-13
Deposition Author(s): Monteiro, D.C.F., Webb, M.E., Pearson, A.R.
Funding Organization(s): Wellcome Trust, German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.137
R-Value Work: 0.113
R-Value Observed: 0.115

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

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

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

(2017) Biochemistry 56: 4931-4939

PubMed: 28832133 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.7b00509
Primary Citation of Related Structures:
5LS7

PubMed 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.

Organizational Affiliation

Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K.

Macromolecule Content

Total Structure Weight: 33.05 kDa
Atom Count: 2,506
Modelled Residue Count: 255
Deposited Residue Count: 280
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate 1-decarboxylase	A	41	Escherichia coli K-12	Mutation(s): 0 Gene Names: panD, b0131, JW0127 EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790 Go to UniProtKB: P0A790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A790
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PanD maturation factor	B	137	Escherichia coli K-12	Mutation(s): 0 Gene Names: panM, panZ, yhhK, b3459, JW3424
UniProt
Find proteins for P37613 (Escherichia coli (strain K12)) Explore P37613 Go to UniProtKB: P37613
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37613
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate 1-decarboxylase	C [auth D]	102	Escherichia coli K-12	Mutation(s): 0 Gene Names: panD, b0131, JW0127 EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790 Go to UniProtKB: P0A790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A790
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain E [auth B] MOL2 format, chain M [auth D] MOL2 format, chain E [auth B]	E [auth B], M [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain M [auth D] Interactions & Density Focus chain E [auth B] Focus chain M [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain J [auth D] MOL2 format, chain D [auth B] MOL2 format, chain J [auth D]	D [auth B], J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain J [auth D] Interactions & Density Focus chain D [auth B] Focus chain J [auth D]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	K [auth D], L [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain K [auth D] Focus chain L [auth D]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D]	H [auth B], I [auth B], O [auth D]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
74C Query on 74C Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D]	N [auth D]	methyl radical C H₃ VNWKTOKETHGBQD-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	C [auth D]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
ACO	Binding MOAD: 5LS7	Kd: 524 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.137
R-Value Work: 0.113
R-Value Observed: 0.115
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.863	α = 90
b = 85.863	β = 90
c = 80.055	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Monteiro, D.C.F.

Webb, M.E.

Pearson, A.R.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	096684/Z/11/Z
Wellcome Trust	United Kingdom	105615/Z/14/Z
German Research Foundation	Germany	Excellence Cluster: Hamburg Centre for Ultrafast Imaging
Wellcome Trust	United Kingdom	094232/Z/10/Z

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2017-09-20
Changes: Database references
Version 1.2: 2017-09-27
Changes: Database references
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-01-17
Changes: Refinement description