1M34

Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4 Stabilized structure

Schmid, B.Einsle, O.Chiu, H.-J.Willing, A.Yoshida, M.Howard, J.B.Rees, D.C.

(2002) Biochemistry 41: 15557-15565

  • DOI: 10.1021/bi026642b
  • Primary Citation of Related Structures:  
    1M34, 1M1Y

  • PubMed Abstract: 
  • The transient formation of a complex between the component Fe- and MoFe-proteins of nitrogenase represents a central event in the substrate reduction mechanism of this enzyme. Previously, we have isolated an N-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide (EDC) cross-linked complex of these proteins stabilized by a covalent isopeptide linkage between Glu 112 and Lys beta400 of the Fe-protein and MoFe-protein, respectively [Willing, A ...

    The transient formation of a complex between the component Fe- and MoFe-proteins of nitrogenase represents a central event in the substrate reduction mechanism of this enzyme. Previously, we have isolated an N-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide (EDC) cross-linked complex of these proteins stabilized by a covalent isopeptide linkage between Glu 112 and Lys beta400 of the Fe-protein and MoFe-protein, respectively [Willing, A., et al. (1989) J. Biol. Chem. 264, 8499-8503; Willing, A., and Howard, J. B. (1990) J. Biol. Chem. 265, 6596-6599]. We report here the biochemical and structural characterization of the cross-linked complex to assess the mechanistic relevance of this species. Glycinamide inhibits the cross-linking reaction, and is found to be specifically incorporated into Glu 112 of the Fe-protein, without detectable modification of either of the neighboring residues (Glu 110 and Glu 111). This modified protein is still competent for substrate reduction, demonstrating that formation of the cross-linked complex is responsible for the enzymatic inactivation, and not the EDC reaction or the modification of the Fe-protein. Crystallographic analysis of the EDC-cross-linked complex at 3.2 A resolution confirms the site of the isopeptide linkage. The nature of the protein surfaces around the cross-linking site suggests there is a strong electrostatic component to the formation of the complex, although the interface area between the component proteins is small. The binding footprints between proteins in the cross-linked complex are adjacent, but with little overlap, to those observed in the complex of the nitrogenase proteins stabilized by ADP-AlF(4)(-). The results of these studies suggest that EDC cross-linking traps a nucleotide-independent precomplex of the nitrogenase proteins driven by complementary electrostatic interactions that subsequently rearranges in a nucleotide-dependent fashion to the electron transfer competent state observed in the ADP-AlF(4)(-) structure.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering 114-96, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase Molybdenum-Iron Protein alpha chainA, C, I, K491Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase Molybdenum-Iron Protein beta chainB, D, J, L522Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase Iron Protein 1E, F, G, H, M, N, O, P289Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifH1
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFM
Query on CFM

Download Ideal Coordinates CCD File 
NA [auth I], R [auth A], RA [auth K], V [auth C]FE-MO-S CLUSTER
Fe7 Mo S9
UZRXIPMKRKMLQF-VGXFRCDIAP
 Ligand Interaction
CLF
Query on CLF

Download Ideal Coordinates CCD File 
PA [auth J], T [auth B], TA [auth L], X [auth D]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth N], BA [auth E], EA [auth F], EB [auth O], HB [auth P], IA [auth G], LA [auth H], XA [auth M]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth E], DB [auth O], HA [auth G], WA [auth M]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HCA
Query on HCA

Download Ideal Coordinates CCD File 
MA [auth I], Q [auth A], QA [auth K], U [auth C]3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
CB [auth O], DA [auth F], GA [auth G], GB [auth P], KA [auth H], VA [auth M], Z [auth E], ZA [auth N]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
OA [auth J], S [auth B], SA [auth L], W [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth O], CA [auth F], FA [auth G], FB [auth P], JA [auth H], UA [auth M], Y [auth E], YA [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 326.1α = 90
b = 75.8β = 102.6
c = 312.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Structure summary
  • Version 1.4: 2019-11-20
    Changes: Advisory, Derived calculations