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Structure of IDP01011

Serine hydroxymethyltransferase from Salmonella typhimurium

Edit deposit information
CSGID target
IDP01011 
PDB Id
3GBX (NCBI MMDB
Authors
J.Osipiuk,B.Nocek,M.Zhou,J.Stam,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Feb 20, 2009 
Release Date
Mar 10, 2009 

Annotation

Description
Serine hydroxymethyltransferase (SHMT) is also called as serine aldolase. It is a pyridoxal-phosphate (PLP) dependent enzyme that plays a central role in the onecarbon metabolism. It catalyzes the reversible inter-conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate, a key intermediate in the biosynthesis of purine, thymidine, choline, and methionine. In addition to this physiological reaction, SHMT has also been shown to catalyze THF-independent aldolytic cleavage, decarboxylation, racemization, and transamination reactions. The PLP dependent enzymes can be classified based on structure and sequence analysis into five major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V). Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer. The importance of SHMT in DNA synthesis together with the high level of enzyme activity in rapidly proliferating cells has focused attention on SHMT as a potential drug target. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
ACT
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=73.95Å, b=49.73Å, c=94.74Å
α=90.00, β=110.67, γ=90.00 
Solvent content
30  
Matthews coefficient
1.77  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
45.50-1.80Å (1.84-1.80Å)  
Rall(%)
15.4 
Rwork(%)
15.2 (21.1) 
Rfree(%)
19.1 (27.5) 
Num. observed reflections
60036 (4193) 
Num. Rfree reflections
3001 (218) 
Completeness(%)
99.4 (93.7) 

Model parameters

Num Atoms
6646  
Num Waters
449  
Num Hetatoms
0  
Model mean isotropic B factor
13.300Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.662°  
Filename uploaded
idp01011.pdb (uploaded on Feb 25, 2009 4:57 PM)  
Inserted
Feb 25, 2009