4GJI

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose

• PDB DOI: https://doi.org/10.2210/pdb4GJI/pdb

• Classification: ISOMERASE
• Organism(s): Stutzerimonas stutzeri
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-09 Released: 2012-12-12 
• Deposition Author(s): Yoshida, H., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.195 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Literature

Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.

Yoshida, H., Yoshihara, A., Teraoka, M., Yamashita, S., Izumori, K., Kamitori, S.

(2013) FEBS Open Bio 3: 35-40

• PubMed: 23772372 
• DOI: https://doi.org/10.1016/j.fob.2012.11.008
• Primary Citation of Related Structures:  
  4GJI, 4GJJ


• PubMed Abstract: 
  

  l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. To elucidate this mechanism, we determined X-ray structures of a mutant l-RhI in complex with l-rhamnopyranose and d-allopyranose. Results suggest that a catalytic water molecule, which acts as an acid/base catalyst in the isomerization reaction, is likely to be involved in pyranose-ring opening, and that a newly found substrate sub-binding site in the vicinity of the catalytic site may recognize different anomers of substrates.

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Organizational Affiliation: 

Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 194.28 kDa 
• Atom Count: 15,195 
• Modelled Residue Count: 1,688 
• Deposited Residue Count: 1,752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-rhamnose isomerase	A, B, C, D	438	Stutzerimonas stutzeri	Mutation(s): 2  Gene Names: L-RhI EC: 5.3.1.14
UniProt
Find proteins for Q75WH8 (Stutzerimonas stutzeri) Explore Q75WH8  Go to UniProtKB:  Q75WH8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RM4	I [auth B], L [auth B], T [auth D]	beta-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-YJRYQGEOSA-N
RAM	F [auth A], K [auth B], P [auth C], V [auth D]	alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N
RNS	E [auth A], J [auth B], O [auth C], U [auth D]	L-RHAMNOSE C6 H12 O5 PNNNRSAQSRJVSB-BXKVDMCESA-N
MN	G [auth A], H [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.195 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.124	α = 90
b = 104.917	β = 106.01
c = 112.376	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Yoshida, H., Kamitori, S.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2014-05-28
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary