3FPF | pdb_00003fpf

Crystal Structure of MtNAS in complex with MTA and tNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea

Dreyfus, C.Lemaire, D.Mari, S.Pignol, D.Arnoux, P.

(2009) Proc Natl Acad Sci U S A 106: 16180-16184

  • DOI: https://doi.org/10.1073/pnas.0904439106
  • Primary Citation Related Structures: 
    3FPE, 3FPF, 3FPG, 3FPH, 3FPJ

  • PubMed Abstract: 

    Nicotianamine (NA), a small molecule ubiquitous in plants, is an important divalent metal chelator and the main precursor of phytosiderophores. Nicotianamine synthase (NAS) is the enzyme catalyzing NA synthesis by the condensation of three aminopropyl moieties of S-adenosylmethionine (SAM) and the cyclization of one of them to form an azetidine ring. Here we report five crystal structures of an archaeal NAS from Methanothermobacter thermautotrophicus, either free or in complex with its product(s) and substrate(s). These structures reveal a two-domains fold arrangement of MtNAS, a small molecule related to NA (named here thermoNicotianamine or tNA), and an original mechanism of synthesis in a buried reaction chamber. This reaction chamber is open to the solvent through a small inlet, and a single active site allows the selective entrance of only one substrate at a time that is then processed and translocated stepwise.


  • Organizational Affiliation
    • Laboratoire de Bioénergétique Cellulaire and Laboratoire des Interactions Protéine Métal, Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institute of Environmental Biology and Biotechnology, Saint-Paul-lez-Durance, F-13108, France.

Macromolecule Content 

  • Total Structure Weight: 69.15 kDa 
  • Atom Count: 4,862 
  • Modeled Residue Count: 528 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B
298Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
Gene Names: MTH675
UniProt
Find proteins for O26771 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26771 
Go to UniProtKB:  O26771
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26771
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on TNA



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
N-[(3S)-3-{[(3S)-3-amino-3-carboxypropyl]amino}-3-carboxypropyl]-L-glutamic acid
C13 H23 N3 O8
PCXSNYIAEDAACL-CIUDSAMLSA-N
MTA

Query on MTA



Download:Ideal Coordinates CCD File
D [auth A],
F [auth B]
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
G [auth B],
H [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.41α = 90
b = 68.74β = 90
c = 146.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary