2UYT | pdb_00002uyt

Structure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.

• PDB DOI: https://doi.org/10.2210/pdb2UYT/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-13 Released: 2007-06-26 
• Deposition Author(s): Grueninger, D., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Substrate Spectrum of L-Rhamnulose Kinase Related to Models Derived from Two Ternary Complex Structures.

Grueninger, D., Schulz, G.E.

(2007) FEBS Lett 581: 3127

• PubMed: 17568582 
• DOI: https://doi.org/10.1016/j.febslet.2007.05.075
• Primary Citation Related Structures: 
  2UYT


• PubMed Abstract: 
  

  The enzyme L-rhamnulose kinase from Escherichia coli participates in the degradation pathway of L-rhamnose, a common natural deoxy-hexose. The structure of the enzyme in a ternary complex with its substrates ADP and L-rhamnulose has been determined at 1.55A resolution and refined to R(cryst)/R(free) values of 0.179/0.209. The result was compared with the lower resolution structure of a corresponding complex containing L-fructose instead of L-rhamnulose. In light of the two established sugar positions and conformations, a number of rare sugars have been modeled into the active center of L-rhamnulose kinase and the model structures have been compared with the known enzymatic phosphorylation rates. Rare sugars are of rising interest for the synthesis of bioactive compounds.

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Organizational Affiliation: 
• Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 54.55 kDa 
• Atom Count: 4,143 
• Modeled Residue Count: 479 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHAMNULOKINASE	A	489	Escherichia coli BL21(DE3)	Mutation(s): 3  EC: 2.7.1.5
UniProt
Find proteins for Q1R415 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R415  Go to UniProtKB:  Q1R415

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
LRH	B [auth A]	6-deoxy-beta-L-fructofuranose C6 H12 O5 CJJCPDZKQKUXSS-AZGQCCRYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.043	α = 90
b = 51.093	β = 90
c = 158.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Grueninger, D., Schulz, G.E.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-10-24
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-09
  Changes: Structure summary