Results 5

STRUCTURE

Quality of YlqF protein model and overall structure

The asymmetric unit of Bacillus subtilis YlqF protein consists of a polymer containing 282 amino acids (Figure 1). The protein has been refined at 2 angstroms to a crystallographic R factor of 21.6% and free R factor of 25%. Table 1 summarizes the refinement statistics including protein quality parameters. MolProbity Ramachandran analysis of YlqF shows that 96.5% of all residues lie in the favoured regions and 98.8% of all residues lie in the allowed regions.

Table 1. Crystal parameters and refinement statistics

Parameters

Resolution[Å] 2.00

R factor, % 21.6

Free R factor, % 25.0

Space Group P 21 21 21

Unit Cell	Length[Å] Angles [°]	a alpha	36.75 90.00	b beta	68.57 90.00	c gamma	105.57 90.00

  1 - MTIQWFPGHM AKARREVTEK LKLIDIVYEL VDARIPMSSR NPMIEDILKN KPRIMLLNKA
 61 - DKADAAVTQQ WKEHFENQGI RSLSINSVNG QGLNQIVPAS KEILQEKFDR MRAKGVKPRA
121 - IRALIIGIPN VGKSTLINRL AKKNIAKTGD RPGITTSQQW VKVGKELELL DTPGILWPKF
181 - EDELVGLRLA VTGAIKDSII NLQDVAVFGL RFLEEHYPER LKERYGLDEI PEDIAELFDA
241 - IGEKRGCLMS GGLINYDKTT EVIIRDIRTE KFGRLSFEQP TM

Figure 1. Amino acid sequence of YlqF

The secondary structure of YlqF mainly contains 50% helical (13 helices; 142 residues) and 10% beta sheet (6 strands; 31 residues)(see Figure 2). YlqF protein consists of two domains. One domain contains Rossmann fold with α/β class. This domain possesses 1-177 residues, and forms a 3-layer sandwich structure. The other one is referred to as a conserved hypothetical protein with mainly α class. This possesses 178-282 residues, and forms a orthogonal bundle structure. YlqF is also classified as a signalling protein. The molecular weight of the protein is 31986 Da.

= pi helix, = 310 helix, = extended strand, = turn, = alpha helix,

Greyed out residues have no structural information

Figure 2. Sequence and Secondary Structure

Structure Analysis

Structure classification of proteins (SCOP) classified YlqF as shown in Table 2. The results of Pfam classification described YlqF as GTPase of unknown function, Rhomboid family, and catalytic domain of alpha amylase.

Class Alpha and beta proteins

Fold P-loop containing nucleoside triphosphate hydrolases

Superfamily P-loop containing nucleoside triphosphate hydrolases

Family G proteins

Domain Probable GTPase YlqF

Species Bacillus subtilis

 No Chain  raw-score Z-score %id lali rmsd  Description
 1 1pujA     3946.0    42.7 100  261  0.0  CONSERVED HYPOTHETICAL PROTEIN YLQF                                             
 2 1udxA      618.8     6.2  14  141 25.5  THE GTP-BINDING PROTEIN OBG                                                     
 3 1uadA      541.8     6.1   9   99  2.6  RAS-RELATED PROTEIN RAL-A                                                       
 4 1zbdA      553.7     6.1  12   99  2.8  RAB-3A                                                                          
 5 1g17A      526.0     5.9  18   95  2.5  RAS-RELATED PROTEIN SEC4                                                        
 6 1c1yA      515.7     5.8  12   96  2.8  RAS-RELATED PROTEIN RAP-1A                                                      
 7 1kjzA      571.3     5.7  14  114  4.0  EIF2GAMMA                                                                       
 8 1oixA      510.9     5.4  11   94  2.6  RAS-RELATED PROTEIN RAB-11A                                                     
 9 1ukvY      519.2     5.3  10   99  2.8  SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR                                    
10 1ijfA      535.8     5.3  13  103  3.6  ELONGATION FACTOR 1-ALPHA                                                       
11 1gpmA      481.7     5.2   7  117  4.0  GMP SYNTHETASE                                                                  
12 1hrkA      483.7     5.1   5  116  4.2  FERROCHELATASE                                                                  
13 1d5cA      474.4     5.1  10   92  2.6  RAB6 GTPASE                                                                     
14 1ni5A      512.4     5.0   6  115  5.5  PUTATIVE CELL CYCLE PROTEIN MESJ                                                
15 3rapS      484.1     5.0   9   92  2.6  G PROTEIN RAP2A                                                                 
16 1gwnA      475.5     5.0  10   94  2.7  RHO-RELATED GTP-BINDING PROTEIN RHOE                                            
17 1vg8A      479.0     5.0  11  106  3.9  RAS-RELATED PROTEIN RAB-7                                                       
18 1cqxA      438.8     4.9   4  116  4.2  FLAVOHEMOPROTEIN                                                                
19 1mkyA      460.7     4.7  11  100  8.8  PROBABLE GTP-BINDING PROTEIN ENGA                                               
20 1fzqA      463.8     4.7  14   92  2.6  ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3

Table . Dali search results of PDB/chain identifiers and structural alignment statistics