Structure of IDP92645

Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli

Edit deposit information
CSGID target
IDP92645 
PDB Id
4QVT (NCBI MMDB
Authors
E.V.Filippova,G.Minasov,G.Winsor,I.Dubrovska,L.Shuvalova,A.J.Wolfe,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ekaterina Filippova 
Responsible lab
Northwestern University 
Deposition Date
Jul 15, 2014 
Release Date
Jul 30, 2014 

Annotation

Description
The acyl-CoA N-acyltransferase domain (ypeA) of putative acyltransferase from Escherichia coli str. K-12 substr. MG1655 was co-crystallized with acyl-CoA, and its structure was determined by molecular replacement and refined to 1.95 A resolution. The P21 asymmetric unit contains 8 copies of the domain. Each chain binds acyl-CoA at the solvent exposed groove between oligomerization and core subdomains (see Annotation for apo-structure; PDB entry 4qus). Acyl-CoA occupies only half of the groove’s length (about 40 A). While the nucleotide portion of the ligand is positioned between the helix from the oligomerization subdomain and two helices from the core subdomain (at one end of the groove; an area of positive surface charge distribution), the aliphatic tail of the ligand extends along the groove into a small pocket that accommodates the acetyl group. Another end of the groove ends with heavily positively charged surface area.  
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
SO4 crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=67.33Å, b=139.97Å, c=75.36Å
α=90.00, β=112.11, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
69.98-1.95Å (2.00-1.95Å)  
Rall(%)
19.0 
Rwork(%)
18.8 (25.8) 
Rfree(%)
23.2 (29.4) 
Num. observed reflections
92393 (6311) 
Num. Rfree reflections
4619 (324) 
Completeness(%)
98.1 (91.0) 

Model parameters

Num Atoms
9199  
Num Waters
243  
Num Hetatoms
705  
Model mean isotropic B factor
55.080Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.871°  
Filename uploaded
4QVT.pdb (uploaded on Jul 30, 2014 3:43 PM)  
Inserted
Jul 30, 2014