6OH9 | pdb_00006oh9

Yeast Guanine Deaminase

• PDB DOI: https://doi.org/10.2210/pdb6OH9/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-05 Released: 2019-07-24 
• Deposition Author(s): Shek, R.S., French, J.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.156 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily.

Shek, R., Hilaire, T., Sim, J., French, J.B.

(2019) Biochemistry 58: 3280-3292

• PubMed: 31283204 
• DOI: https://doi.org/10.1021/acs.biochem.9b00341
• Primary Citation Related Structures: 
  6OH9, 6OHA, 6OHB, 6OHC


• PubMed Abstract: 
  

  Guanine deaminase is a metabolic enzyme, found in all forms of life, which catalyzes the conversion of guanine to xanthine. Despite the availability of several crystal structures, the molecular determinants of substrate orientation and mechanism remain to be elucidated for the amidohydrolase family of guanine deaminase enzymes. Here, we report the crystal structures of Escherichia coli and Saccharomyces cerevisiae guanine deaminase enzymes (EcGuaD and Gud1, respectively), both members of the amidohydrolase superfamily. EcGuaD and Gud1 retain the overall TIM barrel tertiary structure conserved among amidohydrolase enzymes. Both proteins also possess a single zinc cation with trigonal bipyrimidal coordination geometry within their active sites. We also determined a liganded structure of Gud1 bound to the product, xanthine. Analysis of this structure, along with kinetic data of native and site-directed mutants of EcGuaD, identifies several key residues that are responsible for substrate recognition and catalysis. In addition, after a small library of compounds had been screened, two guanine derivatives, 8-azaguanine and 1-methylguanine, were identified as EcGuaD substrates. Interestingly, both EcGuaD and Gud1 also exhibit secondary ammeline deaminase activity. Overall, this work details key structural features of substrate recognition and catalysis of the amidohydrolase family of guanine deaminase enzymes in support of our long-term goal to engineer these enzymes with altered activity and substrate specificity.

---

Organizational Affiliation: 
• Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States.
Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.38 kDa 
• Atom Count: 4,083 
• Modeled Residue Count: 452 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yeast Guanine Deaminase	A	489	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: GUD1, YDL238C EC: 3.5.4.3
UniProt
Find proteins for Q07729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07729  Go to UniProtKB:  Q07729

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	G [auth A], H [auth A], I [auth A], J [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.156 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.229	α = 90
b = 107.229	β = 90
c = 114.831	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Shek, R.S., French, J.B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM124898
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103403

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description