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PDBsum entry 3ezw

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
3ezw
Jmol
Contents
Protein chains
(+ 2 more) 498 a.a. *
Ligands
GOL ×8
EDO ×19
Metals
_CL ×8
_MG
Waters ×1526
* Residue conservation analysis
PDB id:
3ezw
Name: Transferase
Title: Crystal structure of a hyperactive escherichia coli glycerol mutant gly230 --> asp obtained using microfluidic crystalli devices
Structure: Glycerol kinase. Chain: a, b, e, g, c, d, f, h. Synonym: atp:glycerol 3-phosphotransferase, glycerokinase, engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: b3926, glpk, jw3897. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.168     R-free:   0.225
Authors: M.J.Anderson,B.Delabarre,P.Dunten,A.T.Brunger,S.R.Quake
Key ref:
M.J.Anderson et al. (2007). Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry, 46, 5722-5731. PubMed id: 17441732 DOI: 10.1021/bi700096p
Date:
23-Oct-08     Release date:   04-Nov-08    
Supersedes: 2p3r
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6F3  (GLPK_ECOLI) -  Glycerol kinase
Seq:
Struc:
502 a.a.
498 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.30  - Glycerol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + glycerol = ADP + sn-glycerol 3-phosphate
ATP
+
glycerol
Bound ligand (Het Group name = GOL)
corresponds exactly
= ADP
+ sn-glycerol 3-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi700096p Biochemistry 46:5722-5731 (2007)
PubMed id: 17441732  
 
 
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.
M.J.Anderson, B.DeLabarre, A.Raghunathan, B.O.Palsson, A.T.Brunger, S.R.Quake.
 
  ABSTRACT  
 
The crystal structure of an Escherichia coli glycerol kinase mutant Gly230 --> Asp (GKG230D) was determined to 2.0 A resolution using a microfluidics based crystallization platform. The crystallization strategy involved a suite of microfluidic devices that characterized the solubility trends of GKG230D, performed nanoliter volume free interface diffusion crystallization experiments, and produced diffraction-quality crystals for in situ data collection. GKG230D displays increased enzymatic activity and decreased allosteric regulation by the glycolytic pathway intermediate fructose 1,6-bisphosphate (FBP) compared to wild-type GK (GKWT). Structural analysis revealed that the decreased allosteric regulation is a result of the altered FBP binding loop conformations in GKG230D that interfere with the wild-type FBP binding site. The altered FBP binding loop conformations in GKG230D are supported through a series of intramolecular loop interactions. The appearance of Asp230 in the FBP binding loops also repositions the wild-type FBP binding residues away from the FBP binding site. Light scattering analysis confirmed GKG230D is a dimer and is resistant to tetramer formation in the presence of FBP, whereas GKWT dimers are converted into putatively inactive tetramers in the presence of FBP. GKG230D also provides the first structural evidence for multiple GK monomer conformations in the presence of glycerol and in the absence of a nucleotide substrate and verifies that glycerol binding is not responsible for locking GK into the closed conformation necessary for GK activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19819219 D.W.Pettigrew (2009).
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase.
  Arch Biochem Biophys, 492, 29-39.  
18441029 M.Chruszcz, A.Wlodawer, and W.Minor (2008).
Determination of protein structures--a series of fortunate events.
  Biophys J, 95, 1-9.
PDB code: 3pzw
18301740 S.L.Spurgeon, R.C.Jones, and R.Ramakrishnan (2008).
High throughput gene expression measurement with real time PCR in a microfluidic dynamic array.
  PLoS ONE, 3, e1662.  
18422647 Y.Koga, R.Katsumi, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2008).
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.
  FEBS J, 275, 2632-2643.
PDB code: 2zf5
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.