2P6T | pdb_00002p6t

CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUCINE COMPLEX FROM NEISSERIA MENINGITIDIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.300 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2P6T

This is version 1.5 of the entry. See complete history

Literature

The Structure and Transcriptional Analysis of a Global Regulator from Neisseria meningitidis.

Ren, J.Sainsbury, S.Combs, S.E.Capper, R.G.Jordan, P.W.Berrow, N.S.Stammers, D.K.Saunders, N.J.Owens, R.J.

(2007) J Biological Chem 282: 14655-14664

  • DOI: https://doi.org/10.1074/jbc.M701082200
  • Primary Citation Related Structures: 
    2P5V, 2P6S, 2P6T

  • PubMed Abstract: 

    Neisseria meningitidis, a causative agent of bacterial meningitis, has a relatively small repertoire of transcription factors, including NMB0573 (annotated AsnC), a member of the Lrp-AsnC family of regulators that are widely expressed in both Bacteria and Archaea. In the present study we show that NMB0573 binds to l-leucine and l-methionine and have solved the structure of the protein with and without bound amino acids. This has shown, for the first time that amino acid binding does not induce significant conformational changes in the structure of an AsnC/Lrp regulator although it does appear to stabilize the octameric assembly of the protein. Transcriptional profiling of wild-type and NMB0573 knock-out strains of N. meningitidis has shown that NMB0573 is associated with an adaptive response to nutrient poor conditions reflected in a reduction in major surface protein expression. On the basis of its structure and the transcriptional response, we propose that NMB0573 is a global regulator in Neisseria controlling responses to nutrient availability through indicators of general amino acid abundance: leucine and methionine.


  • Organizational Affiliation
    • Oxford Protein Production Facility and Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 148.35 kDa 
  • Atom Count: 10,095 
  • Modeled Residue Count: 1,244 
  • Deposited Residue Count: 1,296 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator, LRP/AsnC family
A, B, C, D, E
A, B, C, D, E, F, G, H
162Neisseria meningitidis MC58Mutation(s): 2 
Gene Names: NMB0573
UniProt
Find proteins for Q9K0L9 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q9K0L9 
Go to UniProtKB:  Q9K0L9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K0L9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LEU

Query on LEU



Download:Ideal Coordinates CCD File
AA [auth F]
CA [auth G]
GA [auth H]
I [auth A]
M [auth B]
AA [auth F],
CA [auth G],
GA [auth H],
I [auth A],
M [auth B],
P [auth C],
S [auth D],
X [auth E]
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]
Q [auth C]
T [auth D]
U [auth D]
Y [auth E]
J [auth A],
Q [auth C],
T [auth D],
U [auth D],
Y [auth E],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth G]
DA [auth H]
EA [auth H]
FA [auth H]
K [auth B]
BA [auth G],
DA [auth H],
EA [auth H],
FA [auth H],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
R [auth D],
V [auth E],
W [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.300 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.389α = 90
b = 149.771β = 105.68
c = 77.845γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-16
    Changes: Structure summary