PDBsum entry 1r8g

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protein Protein-protein interface(s) links
Ligase PDB id
Protein chains
352 a.a. *
Waters ×656
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Structure and function of ybdk
Structure: Hypothetical protein ybdk. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ybdk, b0581. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.15Å     R-factor:   0.189     R-free:   0.252
Authors: C.Lehmann,V.Doseeva,S.Pullalarevu,W.Krajewski,A.Howard, O.Herzberg,Structure 2 Function Project (S2f)
Key ref:
C.Lehmann et al. (2004). YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays. Proteins, 56, 376-383. PubMed id: 15211520 DOI: 10.1002/prot.20103
24-Oct-03     Release date:   17-Aug-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P77213  (CAAL_ECOLI) -  Putative glutamate--cysteine ligase 2
372 a.a.
352 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glutamate--cysteine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamate + L-cysteine = ADP + phosphate + gamma-L-glutamyl-L- cysteine
+ L-glutamate
+ L-cysteine
+ phosphate
+ gamma-L-glutamyl-L- cysteine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular modified amino acid biosynthetic process   1 term 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1002/prot.20103 Proteins 56:376-383 (2004)
PubMed id: 15211520  
YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.
C.Lehmann, V.Doseeva, S.Pullalarevu, W.Krajewski, A.Howard, O.Herzberg.
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.
  Selected figure(s)  
Figure 2.
Figure 2. Stereoscopic view of the C atom trace of the YbdK monomer. Every 20th amino acid is labeled.
Figure 3.
Figure 3. The structures of YbdK and GS. (a) Ribbon diagram of the YbdK fold. Helices are colored salmon-red, -strands are colored lilac. The N- and C-termini are labeled. (b) Ribbon diagram of the GS fold (based on coordinates from PDB entry code 1FPY) in the same orientation as shown for YbdK. The N-terminal domain (residues 1-100) has not been included. Colored as in (a). (c) Stereoscopic view of the aligned active sites of GS (PDB entry code 1FPY) and YbdK. Oxygen atoms are colored red, nitrogen atoms blue. Carbon atoms of YbdK active site residues are shown in pale red, those of GS in pale green. The ADP and phosphinothricin molecules in 1FPY are colored in gold. The YbdK fold is shown in light gray. The residues are labeled according to the YbdK sequence.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 376-383) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21186348 K.Veeravalli, D.Boyd, B.L.Iverson, J.Beckwith, and G.Georgiou (2011).
Laboratory evolution of glutathione biosynthesis reveals natural compensatory pathways.
  Nat Chem Biol, 7, 101-105.  
20636328 F.A.Cerda-Maira, M.J.Pearce, M.Fuortes, W.R.Bishai, S.R.Hubbard, and K.H.Darwin (2010).
Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis.
  Mol Microbiol, 77, 1123-1135.  
19656298 B.Geissler, A.Bonebrake, K.L.Sheahan, M.E.Walker, and K.J.Satchell (2009).
Genetic determination of essential residues of the Vibrio cholerae actin cross-linking domain reveals functional similarity with glutamine synthetases.
  Mol Microbiol, 73, 858-868.  
18812186 C.C.Franklin, D.S.Backos, I.Mohar, C.C.White, H.J.Forman, and T.J.Kavanagh (2009).
Structure, function, and post-translational regulation of the catalytic and modifier subunits of glutamate cysteine ligase.
  Mol Aspects Med, 30, 86-98.  
19671445 F.Cerda-Maira, and K.H.Darwin (2009).
The Mycobacterium tuberculosis proteasome: more than just a barrel-shaped protease.
  Microbes Infect, 11, 1150-1155.  
19483713 K.H.Darwin (2009).
Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis.
  Nat Rev Microbiol, 7, 485-491.  
  19270755 S.E.Lee, Q.X.Li, and J.Yu (2009).
Diverse protein regulations on PHA formation in Ralstonia eutropha on short chain organic acids.
  Int J Biol Sci, 5, 215-225.  
18719892 T.Johnson, G.L.Newton, R.C.Fahey, and M.Rawat (2009).
Unusual production of glutathione in Actinobacteria.
  Arch Microbiol, 191, 89-93.  
18980670 L.M.Iyer, A.M.Burroughs, and L.Aravind (2008).
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.
  Biol Direct, 3, 45.  
16807942 S.E.Lee, Q.X.Li, and J.Yu (2006).
Proteomic examination of Ralstonia eutropha in cellular responses to formic acid.
  Proteomics, 6, 4259-4268.  
16027359 W.W.Krajewski, T.A.Jones, and S.L.Mowbray (2005).
Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights.
  Proc Natl Acad Sci U S A, 102, 10499-10504.
PDB code: 2bvc
15576349 W.Tian, A.K.Arakaki, and J.Skolnick (2004).
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.
  Nucleic Acids Res, 32, 6226-6239.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.