2FB3 | pdb_00002fb3

Structure of MoaA in complex with 5'-GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.271 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism

Haenzelmann, P.Schindelin, H.

(2006) Proc Natl Acad Sci U S A 103: 6829-6834

  • DOI: https://doi.org/10.1073/pnas.0510711103
  • Primary Citation Related Structures: 
    2FB2, 2FB3

  • PubMed Abstract: 

    The first step in molybdenum cofactor biosynthesis, the conversion of 5'-GTP to precursor Z, an oxygen-sensitive tetrahydropyranopterin is catalyzed by the S-adenosylmethionine (SAM)-dependent enzyme MoaA and the accessory protein MoaC. This reaction involves the radical-initiated intramolecular rearrangement of the guanine C8 atom. MoaA harbors an N-terminal [4Fe-4S] cluster, which is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical (5'-dA*), and a C-terminal [4Fe-4S] cluster presumably involved in substrate binding and/or activation. Biochemical studies identified residues involved in 5'-GTP binding and the determinants of nucleotide specificity. The crystal structure of MoaA in complex with 5'-GTP confirms the biochemical data and provides valuable insights into the subsequent radical reaction. MoaA binds 5'-GTP with high affinity and interacts through its C-terminal [4Fe-4S] cluster with the guanine N1 and N2 atoms, in a yet uncharacterized binding mode. The tightly anchored triphosphate moiety prevents the escape of radical intermediates. This structure also visualizes the L-Met and 5'-dA cleavage products of SAM. Rotation of the 5'-dA ribose and/or conformational changes of the guanosine are proposed to bring the 5'-deoxyadenosyl radical into close proximity of either the ribose C2' and C3' or the guanine C8 carbon atoms leading to hydrogen abstraction.


  • Organizational Affiliation
    • Department of Biochemistry and Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA. petra@csb.sunysb.edu

Macromolecule Content 

  • Total Structure Weight: 81.11 kDa 
  • Atom Count: 5,518 
  • Modeled Residue Count: 653 
  • Deposited Residue Count: 680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum cofactor biosynthesis protein A
A, B
340Staphylococcus aureusMutation(s): 0 
Gene Names: MoaA
EC: 4.1.99.22
UniProt
Find proteins for P69848 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P69848 
Go to UniProtKB:  P69848
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69848
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
G [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B],
L [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
5AD

Query on 5AD



Download:Ideal Coordinates CCD File
H [auth A]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
POP

Query on POP



Download:Ideal Coordinates CCD File
M [auth B]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MET

Query on MET



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.271 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.015α = 90
b = 103.449β = 90
c = 191.217γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SCALEPACKdata scaling
FFTmodel building
REFMACrefinement
FFTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description