4WZA

Asymmetric Nucleotide Binding in the Nitrogenase Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural evidence for asymmetrical nucleotide interactions in nitrogenase.

Tezcan, F.A.Kaiser, J.T.Howard, J.B.Rees, D.C.

(2015) J Am Chem Soc 137: 146-149

  • DOI: 10.1021/ja511945e
  • Primary Citation of Related Structures:  
    4WZA

  • PubMed Abstract: 
  • The roles of ATP hydrolysis in electron-transfer (ET) reactions of the nitrogenase catalytic cycle remain obscure. Here, we present a new structure of a nitrogenase complex crystallized with MgADP and MgAMPPCP, an ATP analogue. In this structure the ...

    The roles of ATP hydrolysis in electron-transfer (ET) reactions of the nitrogenase catalytic cycle remain obscure. Here, we present a new structure of a nitrogenase complex crystallized with MgADP and MgAMPPCP, an ATP analogue. In this structure the two nucleotides are bound asymmetrically by the Fe-protein subunits connected to the two different MoFe-protein subunits. This binding mode suggests that ATP hydrolysis and phosphate release may proceed by a stepwise mechanism. Through the associated Fe-protein conformational changes, a stepwise mechanism is anticipated to prolong the lifetime of the Fe-protein-MoFe-protein complex and, in turn, could orchestrate the sequence of intracomplex ET required for substrate reduction.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chainAC477Azotobacter vinelandiiMutation(s): 1 
Gene Names: nifD
EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chainBD522Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase iron protein 1EFGH276Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifH1
EC: 1.18.6.1
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
ICS
Query on ICS

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A, C
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
 Ligand Interaction
CLF
Query on CLF

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A, C
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
ACP
Query on ACP

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F, H
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
ADP
Query on ADP

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E, G
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

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E, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HCA
Query on HCA

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A, C
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
FE
Query on FE

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B, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.201α = 90
b = 120.412β = 90
c = 264.318γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099813
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM045162

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence