5LS7

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • DOI: 10.1021/acs.biochem.7b00509

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase
A
41Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P0A790 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A790
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PanD maturation factor
B
137Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: panZ (panM, yhhK)
Find proteins for P37613 (Escherichia coli (strain K12))
Go to UniProtKB:  P37613
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase
D
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P0A790 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A790
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

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Download CCD File 
D
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
ACO
Query on ACO

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Download CCD File 
B
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
74C
Query on 74C

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D
methyl radical
C H3
VNWKTOKETHGBQD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CO2
Query on CO2

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Download CCD File 
B, D
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
PVO
Query on PVO
D
L-peptide linkingC3 H6 O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.113 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 85.863α = 90.00
b = 85.863β = 90.00
c = 80.055γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom096684/Z/11/Z
Wellcome TrustUnited Kingdom105615/Z/14/Z
German Research FoundationGermanyExcellence Cluster: Hamburg Centre for Ultrafast Imaging
Wellcome TrustUnited Kingdom094232/Z/10/Z

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Database references