Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 84.51 kDa 
• Atom Count: 6234 
• Modelled Residue Count: 710 
• Deposited Residue Count: 744 
• Unique protein chains: 1

1R8G

Structure and function of YbdK

• PDB DOI: 10.2210/pdb1R8G/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-10-24 Released: 2004-08-17 
• Deposition Author(s): Lehmann, C., Doseeva, V., Pullalarevu, S., Krajewski, W., Howard, A., Herzberg, O., Structure 2 Function Project (S2F)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.189 

Literature

YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays

Lehmann, C., Doseeva, V., Pullalarevu, S., Krajewski, W., Howard, A., Herzberg, O.

(2004) Proteins 56: 376-383

• PubMed: 15211520 
• DOI: 10.1002/prot.20103
• Primary Citation of Related Structures:  
  1R8G


• PubMed Abstract: 
  

The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.

---

Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybdK	A, B	372	Escherichia coli	Mutation(s): 11  Gene Names: ybdK, b0581 EC: 6.3 (PDB Primary Data), 6.3.2.2 (UniProt)
UniProt
Find proteins for P77213 (Escherichia coli (strain K12)) Explore P77213  Go to UniProtKB:  P77213

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.47	α = 90
b = 100.32	β = 99.94
c = 71.37	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-24 
• Released Date: 2004-08-17 
Deposition Author(s): Lehmann, C., Doseeva, V., Pullalarevu, S., Krajewski, W., Howard, A., Herzberg, O., Structure 2 Function Project (S2F)

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-07-28
  Changes: Database references, Derived calculations, Refinement description