User:Jing Liu/Sandbox 1: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
Jing Liu (talk | contribs)
51 edits
New page: frame|Bacterial chemotaxis receptor One of the CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Ch...
 
Jing Liu (talk | contribs)
51 edits
No edit summary
 
(42 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]
One of the [[CBI Molecules]] being studied in the  [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
 
 
==Your Heading Here (maybe something like 'Structure')==<StructureSection load='1dq8' size='300' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''>Anything in this section will appear adjacent to the 3D structure and will be scrollable.
1
 
2
 
2
 
3
 
 
3
 
 
4
 
5
 
5
 
6
 
6
 
7
8
 
8
 
9
 
 
10
 
11
 
12


One of the [[CBI Molecules]] being studied in the  [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].


Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."
</StructureSection>
<Structure load='1L8Q' size='300' frame='true' align='right' caption='1L8Q 76-399' scene='User:Jing_Liu/Sandbox_1/1/4' />
This is a <scene name='User:Jing_Liu/Sandbox_1/1/4'>DnaA monomer strucure(residues 76-399)</scene>, which contains an <scene name='User:Jing_Liu/Sandbox_1/1/5'>ADP</scene> in it.


----


A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.
----


{{Clear}}
----
<applet load='1wat' size='[450,338]' frame='true' align='right'
=== DnaA function in Prokaryotes===
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>
DnaA is an AAA+ protein in prokaryotes for DNA replication initiation. To ensure correct timing of DNA replication, intracellular DnaA is under multi-level control, including changing expression/degradation level, regulator control and functional activation/inactivation by nucleotide-depedent conformational change. DnaA is a conserved protein in prokaryotes. In ''E. coli'', There are four regions in this protein[http://www.ncbi.nlm.nih.gov/pubmed/10572294]:


=== Ligand-binding domain ===
I: residues 1-85. DnaB loading domain;


II: residues 86-133. linker region;


III: residues 134-372. ATPase domain;


The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).
IV: residues 373-467. DNA binding domain;




Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.
DnaA function is regulated by different nucleotide binding state. In ATP bound state, DnaA can recognize more binding elements on the chromosome(called DnaA box), and initiate replication by unwinding specific region in the DNA and recruit DnaB helicase. However, after the ATP hydrolysis, DnaA-ADP becomes an inactive protein. This activity change was shown to be associated with its oligomeric assembly state.


=== DnaA Monomer Structure ===
The <scene name='User:Jing_Liu/Sandbox_1/1/4'>structure of DnaA</scene> in ''Aquifex aeolicus'' was solved in 2002[http://www.ncbi.nlm.nih.gov/pubmed/12234917?dopt=Abstract], and it contains the linker region, AAA+ domain and DNA binding domain(DBD). The interaction with DNA is through the recognization of a conserved 9 bp DNA recognition sequence (TTA/TTNCACC), and this was shown by the crystal structure of the <scene name='User:Jing_Liu/Sandbox_1/2/1'>complex</scene> in ''Mycobacterium tuberculosis''[http://www.ncbi.nlm.nih.gov/pubmed/21620858?dopt=Abstract].


{{Clear}}
=== Distinct Assembly State of DnaA ===
<applet load='2ho9' size='[450,338]' frame='true' align='right'
<Structure load='1L8Q' size='300' frame='true' align='right' caption='2HCB tetramer' scene='User:Jing_Liu/Sandbox_1/3/3' />
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>
The crystal structure of AMP-PCP-bound DnaA reveals a <scene name='User:Jing_Liu/Sandbox_1/3/3'>right-handed superhelix</scene> structure[http://www.ncbi.nlm.nih.gov/pubmed/16829961?dopt=Abstract]. Each monomer contact with another two monomers to form a filamentous structure. The engagement of ATP involved the arginine figure at position 230.


=== Chemotaxis adaptor protein CheW ===
=== Reference ===
1. Messer, W., et al., Functional domains of DnaA proteins. Biochimie, 1999. 81(8-9): p. 819-25.


2. Erzberger, J.P., et al., The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J. 2002 Sep 16;21(18):4763-73.


CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.
3. Tsodikov OV and Biswas T. Structural and thermodynamic signatures of DNA recognition by Mycobacterium tuberculosis DnaA. J Mol Biol. 2011 Jul 15;410(3):461-76. Epub 2011 May 18.


At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).
4. Erzberger, J.P., et al., Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol. 2006 Aug;13(8):676-83. Epub 2006 Jul 9.

Latest revision as of 19:01, 10 October 2012

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.


==Your Heading Here (maybe something like 'Structure')==

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

1

2

2

3


3


4

5

5

6

6

7

8

8

9


10

11

12


Structure of HMG-CoA reductase (PDB entry 1dq8)

Drag the structure with the mouse to rotate

1L8Q 76-399

Drag the structure with the mouse to rotate

This is a , which contains an in it.

DnaA function in ProkaryotesDnaA function in Prokaryotes

DnaA is an AAA+ protein in prokaryotes for DNA replication initiation. To ensure correct timing of DNA replication, intracellular DnaA is under multi-level control, including changing expression/degradation level, regulator control and functional activation/inactivation by nucleotide-depedent conformational change. DnaA is a conserved protein in prokaryotes. In E. coli, There are four regions in this protein[1]:

I: residues 1-85. DnaB loading domain;

II: residues 86-133. linker region;

III: residues 134-372. ATPase domain;

IV: residues 373-467. DNA binding domain;


DnaA function is regulated by different nucleotide binding state. In ATP bound state, DnaA can recognize more binding elements on the chromosome(called DnaA box), and initiate replication by unwinding specific region in the DNA and recruit DnaB helicase. However, after the ATP hydrolysis, DnaA-ADP becomes an inactive protein. This activity change was shown to be associated with its oligomeric assembly state.

DnaA Monomer StructureDnaA Monomer Structure

The in Aquifex aeolicus was solved in 2002[2], and it contains the linker region, AAA+ domain and DNA binding domain(DBD). The interaction with DNA is through the recognization of a conserved 9 bp DNA recognition sequence (TTA/TTNCACC), and this was shown by the crystal structure of the in Mycobacterium tuberculosis[3].

Distinct Assembly State of DnaADistinct Assembly State of DnaA

2HCB tetramer

Drag the structure with the mouse to rotate

The crystal structure of AMP-PCP-bound DnaA reveals a structure[4]. Each monomer contact with another two monomers to form a filamentous structure. The engagement of ATP involved the arginine figure at position 230.

ReferenceReference

1. Messer, W., et al., Functional domains of DnaA proteins. Biochimie, 1999. 81(8-9): p. 819-25.

2. Erzberger, J.P., et al., The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J. 2002 Sep 16;21(18):4763-73.

3. Tsodikov OV and Biswas T. Structural and thermodynamic signatures of DNA recognition by Mycobacterium tuberculosis DnaA. J Mol Biol. 2011 Jul 15;410(3):461-76. Epub 2011 May 18.

4. Erzberger, J.P., et al., Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol. 2006 Aug;13(8):676-83. Epub 2006 Jul 9.

Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=User:Jing_Liu/Sandbox_1&oldid=1543513"