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 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C
477Azotobacter vinelandiiMutation(s): 1 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07328
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
522Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07329
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein 1
E, F, G, H
276Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00459
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS
Query on ICS

Download Ideal Coordinates CCD File 
J [auth A],
N [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF
Query on CLF

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K [auth A],
O [auth C]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
ACP
Query on ACP

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U [auth F],
Z [auth H]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
ADP
Query on ADP

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S [auth E],
X [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4
Query on SF4

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Q [auth E],
V [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HCA
Query on HCA

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I [auth A],
M [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
FE
Query on FE

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L [auth B],
P [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

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R [auth E],
T [auth F],
W [auth G],
Y [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • 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
  • Version 1.5: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description