4WZA | pdb_00004wza

Asymmetric Nucleotide Binding in the Nitrogenase Complex

PDB DOI: https://doi.org/10.2210/pdb4WZA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii
Mutation(s): Yes

Deposited: 2014-11-19 Released: 2014-12-31
Deposition Author(s): Tezcan, F.A., Kaiser, J.T., Howard, J.B., Rees, D.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.187 (Depositor), 0.187 (DCC)
R-Value Work:
0.145 (Depositor), 0.146 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 25522159 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja511945e
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 353.03 kDa
Atom Count: 26,654
Modeled Residue Count: 3,092
Deposited Residue Count: 3,102
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	477	Azotobacter vinelandii	Mutation(s): 1 EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii) Explore P07328 Go to UniProtKB: P07328
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	522	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329 Go to UniProtKB: P07329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07329
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein 1	E, F, G, H	276	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii) Explore P00459 Go to UniProtKB: P00459
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00459
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICS Query on ICS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C]	J [auth A], N [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth C]
CLF Query on CLF Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C]	K [auth A], O [auth C]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth C] Interactions & Density Focus chain K [auth A] Focus chain O [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain Z [auth H] MOL2 format, chain U [auth F] MOL2 format, chain Z [auth H] mmCIF format, chain U [auth F] mmCIF format, chain Z [auth H]	U [auth F], Z [auth H]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Focus chain Z [auth H] Interactions & Density Focus chain U [auth F] Focus chain Z [auth H]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain X [auth G] MOL2 format, chain S [auth E] MOL2 format, chain X [auth G] mmCIF format, chain S [auth E] mmCIF format, chain X [auth G]	S [auth E], X [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain S [auth E] Focus chain X [auth G] Interactions & Density Focus chain S [auth E] Focus chain X [auth G]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain V [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain V [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain V [auth G]	Q [auth E], V [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain Q [auth E] Focus chain V [auth G] Interactions & Density Focus chain Q [auth E] Focus chain V [auth G]
HCA Query on HCA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C]	I [auth A], M [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D]	L [auth B], P [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth D] Interactions & Density Focus chain L [auth B] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	R [auth E], T [auth F], W [auth G], Y [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.187 (Depositor), 0.187 (DCC)
R-Value Work: 0.145 (Depositor), 0.146 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.201	α = 90
b = 120.412	β = 90
c = 264.318	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM099813
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM045162

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