Function: Siowwei: Difference between revisions

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== 2.1 Protein-interaction annotation: == ==
'''Results on Function Analysis'''
Protein Functions


2.1 Protein-interaction annotation:
'''[[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.
'''''Table 2.1''''' Complete annotation of NUBP2 retrieved from UnitProtKB/Swiss-Prot


2.2 Sequence analysis (include ClustalW- MinD & NUBP2 sequence alignment):
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. (More explanation on Min Complex in bacteria context) 
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-active sites)
'''Names and origin'''
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. (similar motif were also found in MinD)
 
 
{| class="prettytable"
| Protein names
| '''Nucleotide-binding protein 2''''' Also known as:''     NBP 2
 
|-
| Gene names
|
{| class="prettytable"
| Name: 
| '''NUBP2'''
 
|}
 
 
|-
| Organism
| [http://beta.uniprot.org/taxonomy/9606 Homo sapiens (Human)]
 
|}
'''General annotation (Comments)'''
 
 
{| class="prettytable"
| Function
| May contribute to formation of bipolar spindles (By similarity to ''E.coli'' MinD homolog).
 
|-
| Subunit structure
| Binds NUBP1 and KIFC1 (By similarity).
 
|-
| Subcellular location
| Nucleus (By similarity). Note=Associated with nucleus during interphase and nucleocytoplasm surrounding mitotic spindles during early mitosis. Enriched around centrosomes during late mitosis (By similarity).
 
|-
| Tissue specificity
| Widely expressed with highest expression in skeletal muscle.
 
|-
| Developmental stage
| Expressed in fetal brain, lung, liver and kidney.
 
|-
| Sequence similarities
| Belongs to the [http://beta.uniprot.org/uniprot/?query=family:%22Mrp%2FNBP35+ATP-binding+proteins+family%22 Mrp/NBP35 ATP-binding proteins family].
 
|}
'''Ontologies'''
 
 
{| class="prettytable"
| colspan="2" | '''Keywords'''
 
|-
|    Cellular component
| [http://beta.uniprot.org/keywords/539 Nucleus]
 
|-
|    Ligand
| [http://beta.uniprot.org/keywords/67 ATP-binding][http://beta.uniprot.org/keywords/547 Nucleotide-binding]
 
|-
| colspan="2" | '''Gene Ontology (GO)'''
 
|-
|    Molecular function
| [http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0000166 Nucleotide binding]  
 
Traceable author statement. Source: ProtInc
 
|}
 
 
 
 
'''[[2.2 Sequence Analysis]]'''
 
 
 
'''''Table 2.2 '''''Aligned sequence of 2ph1 protein
 
[[Image:Ali.jpg]]
 
 
'''[[2.3 Sequence motif (domain) analysis]]'''
 
'''''Table 2.3''''' The diagram and table below show the '''3''' sequence motifs found in the sequence
 
 
[[Image:3seq.jpg]]
[[Image:3seq1.jpg]]
 
 
'''''Table 2.4 '''''The diagram and table below show the '''1''' sequence of superfamily found in the sequence
 
 
 
[[Image:seq1.jpg]]
 
[[Image:seq2.jpg]]
 
 
'''[[2.4. Protein-protein interaction]]'''
 
'''''Figure 1.'' '''Protein-protein interactions search using 2ph1 sequence
 
 
<center>[[Image:inter1.jpg]]</center>
 
 
 
 
<center>[[Image:input1.jpg]]</center>
 
'''''Figure 2. '''''Protein-protein interactions search using ''NUBP2 ''sequence
 
 
<center>[[Image:inter2.jpg]]</center>
 
 
 
 
 
<center>[[Image:input2.jpg]]</center>
 
'''[[2.5 Subcellular location]]'''
 
 
'''Figure 3.''' NUBP2 expressions in human and mouse tissues
 
 
[[Image:exp.jpg]]

Latest revision as of 05:37, 10 June 2008

Results on Function Analysis

2.1 Protein-interaction annotation

Table 2.1 Complete annotation of NUBP2 retrieved from UnitProtKB/Swiss-Prot


Names and origin


Protein names Nucleotide-binding protein 2 Also known as:     NBP 2
Gene names
Name:  NUBP2


Organism Homo sapiens (Human)

General annotation (Comments)


Function May contribute to formation of bipolar spindles (By similarity to E.coli MinD homolog).
Subunit structure Binds NUBP1 and KIFC1 (By similarity).
Subcellular location Nucleus (By similarity). Note=Associated with nucleus during interphase and nucleocytoplasm surrounding mitotic spindles during early mitosis. Enriched around centrosomes during late mitosis (By similarity).
Tissue specificity Widely expressed with highest expression in skeletal muscle.
Developmental stage Expressed in fetal brain, lung, liver and kidney.
Sequence similarities Belongs to the Mrp/NBP35 ATP-binding proteins family.

Ontologies


Keywords
   Cellular component Nucleus
   Ligand ATP-bindingNucleotide-binding
Gene Ontology (GO)
   Molecular function Nucleotide binding

Traceable author statement. Source: ProtInc



2.2 Sequence Analysis


Table 2.2 Aligned sequence of 2ph1 protein

Ali.jpg


2.3 Sequence motif (domain) analysis

Table 2.3 The diagram and table below show the 3 sequence motifs found in the sequence


3seq.jpg 3seq1.jpg


Table 2.4 The diagram and table below show the 1 sequence of superfamily found in the sequence


Seq1.jpg

Seq2.jpg


2.4. Protein-protein interaction

Figure 1. Protein-protein interactions search using 2ph1 sequence


Inter1.jpg



Input1.jpg

Figure 2. Protein-protein interactions search using NUBP2 sequence


Inter2.jpg



Input2.jpg

2.5 Subcellular location


Figure 3. NUBP2 expressions in human and mouse tissues


Exp.jpg

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