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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 in 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.


Secondary structure.png

Pi helix.gif = pi helix, 310helix.jpg = 310 helix, Sheet.jpg = extended strand, Turn.jpg = turn, Alpha.jpg = 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 results of PDB/chain identifiers and structural alignment statistics