NUBP2D

Discussion

1.Structure analysis Structure analysis showed that the NUBP2(MinD homolog, E.Coli) is like to belong to the membrane associated ATPase family, a significant finding was seen with Dali search analysis. Due to the structure of NUBP2 was not solved, as the structure of 2ph1 from Achaeoglobus fulgidus is 39.66% similar to NUBP2, it was used to search in Dali. Most of the proteins with similar structures to 2ph1 are from this family with similar function. 1.1 The nucleotide binding protein 2ph1 from Achaeoglobus fulgidus is a 240 residue protein with a molecular weight 26087.there are 8 alpha helices 7-14,32-45,61-65,111-122,143-151,167-178,211-217,230-237,and 12 beta strands 83-84,91-93,50-54,131-135,20-24,155-160,184-189,222-225,74-76,79-81,194-195,202-203.. the resolution of 2ph1 is 2.7 Å. The PDB file observed in Pymol shows that the structure of 2ph1 is alpha+beta. The P-loop is started from about residue 9 to 16 “[GA]-X2-(G)-X-G-K-[ST]”. The walker B motifs are around residue 34-49 and residue 117-130. the 3-D structure shows that these motifs form a pocket in the middle of the protein which is the ATP binding site. 1.2 From the Dali result, the protein1g3q has the highest Z-score (20) and 21% similarity with 2ph1. The alignment from Pymol of these two protein shows the RMS of 8.55. the high similarity of structure suggested the high similarity of function as a cell division inhibitor. 1g3q also belong to the MinD ATPase family. 1.3 In 2ph1 the P-loop presents as GKGGVGKST. The walker B motif is presents as LDADFLG. These motifs are characteristic features of ATPase as they comprise important nucleotide binding and intramolecular signaling domains in P-loop ATPase.

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2.Funtion analysis 2.1 Protein-interaction annotation:

Exploration of existing database on UnitProtKB/Swiss-Prot annotated the relationship of NUBP2 and MinD. This data similarity search detected closely related sequences from other species, and their annotation give the first clue regarding a possible function inferred from the known function of related sequences. Similar sequences originated from different species- and in an order consistent with evolutionary distance may be considered potentially orthologous.

2.2 Sequence analysis (include ClustalW):

UniProt database searches with 2ph1 (chain A) amino acid sequences indicated the sequence homology between MinD (MRP, in prokaryote) and NUBP (NBP, in eukaryote). Sequence similarity searches showed a likely relationship to the E. coli MinD gene in 48-45% of the amino acid position (Table 3). MinD gene is a membrane-associated ATPase that inhibits cell division at the poles and consequently induces normal cell division. Based on the similarity, the function of NUBP2 is predicted to involve in cell division. The remarkable alignment score illustrated the evolutionary distance between E. coli and human. Due to the similarity between NUBP2 and MinD, we favor the hypothesis that NUBP2 participates in regulating cell division and poses the characteristic of ATP-binding protein.

Research conducted by Shahrestanifar et al. in 1994 investigated the expression of rat homolog of NUBP2 in several cell lines; it was found that NUBP2 was presence in all samples. Highest expression of NUBP2 was found in human adult’s lung, testis and skeletal tissues followed by kidney, brain, spleen and heart (Nakashima et al., 1999). Another research conducted by Unger and Hartwell in 1976 demonstrated mutation of the gene was found to be lethal, indicating the NUBP2 plays a vital role in cell division.

2.3 Sequence motif (domain) analysis: (include 3D structural analysis)

Results returned from InterProScan indicate this nucleotide binding protein (NBP) shares a characteristic motif with the ATPase superfamily (Table 1). Additionally, a characteristic sequence motif “[GA]-X2-(G)-X-G-K-[ST]” called the phosphate binding group (p-loop) was identified (Table 2). Many biologically processes are thermodynamically unfavorable, and therefore cannot occur without the use of an extra source of energy. In many cases, this source of energy comes from the hydrolysis of adenosine triphosphate (ATP) molecules. Based on its ATP binding motif, this gene was called nucleotide-binding protein (NBP). Therefore, NBP is also known as ATP-binding domain.

2.4. Protein-protein interaction (maybe evolution):

Regardless of function, proteins seldom act alone and are usually assembled into complexes and dynamic macromolecular structures to perform their task in the cell. The majority of the interacting proteins (up to 70-80%) share at least one function (Lane et al., 2007). This property is used to assign a function to the given protein based on the functions of its characterized binding partners. In-silico analysis using String database showed that Methionyl-tRNA synthetase function is conserved between prokaryotes and eukaryotes (as highlighted in Figure 1 and 2). This annotated function is supported by the studies done by Unger and Hartwell. Their experiments concluded the necessity of Methionyl-tRNA synthetase to control cell division in yeast. Hence, it supported our hypothesis that NUBP2 has a vital role in regulation of cell division (cytokinesis).

2.5 Subcellular location:

The returned results from GNF SymAtlas database showed that human and mouse NUBP2 protein is expressed in all range of cell. Highest expression of this protein is found in lung, liver, spleen, testis and skeletal tissues as they involve in cell repair and cell division. NUBP2 belongs to nucleotide-binding proteins family; it is required to hydrolyse ATP to drive an energetically unfavorable reaction into thermodynamically favorable one. The minimum expression of NUBP2 in other tissues explains that other nucleotide-binding protein family might be up-regulated in certain tissues, for example NUBP1 which is highly expressed in spleen and eye organs.