3K3T | pdb_00003k3t

E185A mutant of peptidoglycan hydrolase from Sphingomonas sp. A1

• PDB DOI: https://doi.org/10.2210/pdb3K3T/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp. A1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-04 Released: 2010-07-14 
• Deposition Author(s): Maruyama, Y., Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1

Maruyama, Y., Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

(2010) J Basic Microbiol 50: 311-317

• PubMed: 20586063 
• DOI: https://doi.org/10.1002/jobm.200900249
• Primary Citation Related Structures: 
  3K3T


• PubMed Abstract: 
  

  The flagellar protein FlgJ, a member of glycoside hydrolase family 73, has N- and C-terminal domains that are responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. The crystal structure of the C-terminal domain of SPH1045 (SPH1045-C), the FlgJ from Sphingomonas sp. strain A1, showed a long cleft formed by two lobes, alpha and beta. In this study, seven site-specific mutants of residues in the cleft were prepared and analyzed. Enzyme activity was reduced most significantly in mutants E185A and Y281A, followed by E224A. A comparison of the crystal structure of the inactive mutant E185A with that of other related enzymes revealed that Glu185 is structurally reasonable as the proton donor and that Tyr281 is close to Glu185. Glu224 is, however, far from the catalytic site, which is inconsistent with the decreased activity exhibited by E224A. The structural flexibility of Glu224 and its neighboring residues observed in SPH1045-C may indicate that this region is able to change its conformation upon substrate binding.

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Organizational Affiliation: 
• Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.86 kDa 
• Atom Count: 1,317 
• Modeled Residue Count: 152 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan hydrolase FlgJ	A	170	Sphingomonas sp. A1	Mutation(s): 3  Gene Names: flgJ EC: 3.2.1
UniProt
Find proteins for B7XH69 (Sphingomonas sp. A1) Explore B7XH69  Go to UniProtKB:  B7XH69

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.441	α = 90
b = 54.441	β = 90
c = 101.569	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Maruyama, Y., Ochiai, A., Itoh, T., Mikami, B., Hashimoto, W., Murata, K.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description