3NIO

Crystal structure of Pseudomonas aeruginosa guanidinobutyrase

• PDB DOI:  https://doi.org/10.2210/pdb3NIO/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-16 Released: 2011-06-01 
• Deposition Author(s): Lee, S.J., Kim, H.S., Kim, D.J., Yoon, H.J., Kim, K.H., Yoon, J.Y., Jang, J.Y., Im, H., An, D., Suh, S.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Literature

Crystal structures of Pseudomonas aeruginosa guanidinobutyrase and guanidinopropionase, members of the ureohydrolase superfamily

Lee, S.J., Kim, D.J., Kim, H.S., Lee, B.I., Yoon, H.J., Yoon, J.Y., Kim, K.H., Jang, J.Y., Im, H.N., An, D.R., Song, J.S., Kim, H.J., Suh, S.W.

(2011) J Struct Biol 175: 329-338

• PubMed: 21600989 
• DOI: https://doi.org/10.1016/j.jsb.2011.05.002
• Primary Citation of Related Structures:  
  3NIO, 3NIP, 3NIQ


• PubMed Abstract: 
  

Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA) catalyze the hydrolysis of 4-guanidinobutyrate and 3-guanidinopropionate, respectively. They belong to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase. In this study, we have determined the crystal structures of GbuA and GpuA from P. aeruginosa to provide a structural insight into their substrate specificity. Although GbuA and GpuA share a common structural fold of the typical ureohydrolase superfamily, they exhibit significant variations in two active site loops. Mutagenesis of Met161 of GbuA and Tyr157 of GpuA, both of which are located in the active site loop 1 and predicted to be involved in substrate recognition, significantly affected their enzymatic properties, implying their important roles in catalysis.

---

Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 210.4 kDa 
• Atom Count: 15,530 
• Modelled Residue Count: 1,896 
• Deposited Residue Count: 1,914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanidinobutyrase	A, B, C, D, E, F	319	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: gbuA, PA1421 EC: 3.5.3.7
UniProt
Find proteins for Q9I3S3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I3S3  Go to UniProtKB:  Q9I3S3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C, D, E, F	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.047	α = 90
b = 158.954	β = 114.84
c = 84.547	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Lee, S.J., Kim, H.S., Kim, D.J., Yoon, H.J., Kim, K.H., Yoon, J.Y., Jang, J.Y., Im, H., An, D., Suh, S.W.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-26
  Changes: Database references