8WZU | pdb_00008wzu

4-hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.

• PDB DOI: https://doi.org/10.2210/pdb8WZU/pdb
• Entry: 8WZU supersedes: 8IUP

• Classification: LIGASE
• Organism(s): Nitrosopumilus maritimus SCM1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-02 Released: 2024-06-12 
• Deposition Author(s): Johnson, J., Demirci, H.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus.

Johnson, J., Tolar, B.B., Tosun, B., Yoshikuni, Y., Francis, C.A., Wakatsuki, S., DeMirci, H.

(2024) Commun Biol 7: 1364-1364

• PubMed: 39433970 
• DOI: https://doi.org/10.1038/s42003-024-06432-x
• Primary Citation of Related Structures:  
  8WZU


• PubMed Abstract: 
  

  The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Koç University, Istanbul, Türkiye.
Department of Earth System Science, Stanford University, Stanford, CA, USA.
Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA.
The US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Structural Biology, Stanford University, Stanford, CA, USA. [e-mail].
Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA. [e-mail].
Department of Molecular Biology and Genetics, Koç University, Istanbul, Türkiye. [e-mail].
Stanford PULSE Institute, SLAC, Menlo Park, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 151.65 kDa 
• Atom Count: 9,578 
• Modeled Residue Count: 1,249 
• Deposited Residue Count: 1,396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybutyrate--CoA ligase [ADP-forming]	A, B	698	Nitrosopumilus maritimus SCM1	Mutation(s): 0  Gene Names: Nmar_0206 EC: 6.2.1.56
UniProt
Find proteins for A9A1Y1 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A1Y1  Go to UniProtKB:  A9A1Y1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 356.98	α = 90
b = 70.4	β = 90
c = 75.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Johnson, J., Demirci, H.
• This entry supersedes: 8IUP

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2025-03-12
  Changes: Database references, Structure summary
• Version 1.2: 2025-06-25
  Changes: Database references