User:Xuni Li/Sandbox 1

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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].
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].
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=== Introduction ===
=== Introduction ===
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Bacteria use their receptors to sense the environment to change their swimming patterns. There are different kinds of [http://en.wikipedia.org/wiki/Chemoreceptor chemoreceptors] that respond to different stimuli. The figure on the right is the [http://en.wikipedia.org/wiki/Methyl-accepting_chemotaxis_protein methyl-accepting protein] of Thermotoga maritima receptor. Bacteria like to flee away from the repellent when high concentrations are present in the environment. CheA is a histidine kinase that associates with CheW, an adaptor protein, will cause the flagella to turn clockwise and result in a tumbling motion. On the other hand, when a high concentration of attractants are present in the environment, the CheA kinase will be turned off, cause flagella to turn counterclockwise, resulting in a forward swimming pattern. <ref name="introduction">Hazelbauer, Falke and Parkinson. "Bacterial chemoreceptors: high-performance signaling in networked arrays." Biochemical Sciences, 2007, 33 (1), 9-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18165013]</ref>
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Bacteria use their receptors to sense the environment to change their swimming patterns. There are different kinds of [http://en.wikipedia.org/wiki/Chemoreceptor chemoreceptors] that respond to different stimuli. The figure on the right is the [http://en.wikipedia.org/wiki/Methyl-accepting_chemotaxis_protein methyl-accepting protein] of Thermotoga maritima <scene name='User:Xuni_Li/Sandbox_1/Initial/1'>receptor</scene>. Bacteria like to flee away from the repellent when high concentrations are present in the environment. CheA is a [http://en.wikipedia.org/wiki/Histidine_kinase histidine kinase] that associates with CheW, an [http://en.wikipedia.org/wiki/Adaptor_protein adaptor protein], will cause the flagella to turn clockwise and result in a tumbling motion. On the other hand, when a high concentration of attractants are present in the environment, the CheA kinase will be turned off, cause flagella to turn counterclockwise, resulting in a forward swimming pattern. <ref name="introduction">Hazelbauer, Falke and Parkinson. "Bacterial chemoreceptors: high-performance signaling in networked arrays." Biochemical Sciences, 2007, 33 (1), 9-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18165013]</ref>
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[[Image:Receptor.png]]
===Structure and Functions===
===Structure and Functions===
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[http://en.wikipedia.org/wiki/Chemoreceptor Chemoreceptors] usually contain a periplasmic ligand binding domain, the transmembrane domain, a HAMP domain which is for signal conversion, and the cytoplasmic domain that contains the methylation sites, flexible bundle and protein binding sites where CheA and CheW bind.
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[http://en.wikipedia.org/wiki/Chemoreceptor Chemoreceptors] usually contain a periplasmic ligand binding domain, the transmembrane domain, a [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR003660 HAMP domain] which is for signal conversion, and the cytoplasmic domain that contains the methylation sites, flexible bundle and protein binding sites where CheA and CheW bind.
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CheA is a histidine kinase that contains five units. The P1 domain is the site of substrate [http://en.wikipedia.org/wiki/Autophosphorylation autophosphorylation] that associates with kinase P4 domain, P2 is where phosphate transfers to CheY, another response regulator protein, from P1. P3, P4 and P5 are the dimerization, kinase and the receptor-coupling domains. The P3 domain was predicted to interact with CheW which stabilize the interface between P3 and P5. The NMR structure has shown that P5 is proximal to the CheW β barrel (residues 635-660). <ref name="structure">Park, Borbat, Gonzalez-Bonet, Bhatnagar, et al. "Reconstruction of the chemotaxis receptor-kinase assembly." Nature Structural and Molecular Biology, April 23, 2006, 13 (5), 400-407. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16622408]</ref>
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CheA is a [http://en.wikipedia.org/wiki/Histidine_kinase histidine kinase] that contains five units. The P1 domain is the site of substrate [http://en.wikipedia.org/wiki/Autophosphorylation autophosphorylation] that associates with kinase P4 domain, P2 is where phosphate transfers to CheY, another response regulator protein, from P1. P3, P4 and P5 are the dimerization, kinase and the receptor-coupling domains. The P3 domain was predicted to interact with CheW which stabilize the interface between P3 and P5. The NMR structure has shown that P5 is proximal to the CheW β barrel (residues 635-660). <ref name="structure">Park, Borbat, Gonzalez-Bonet, Bhatnagar, et al. "Reconstruction of the chemotaxis receptor-kinase assembly." Nature Structural and Molecular Biology, April 23, 2006, 13 (5), 400-407. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16622408]</ref> On the right, is the CheW with CheA P4, P5 domains (orange) <scene name='User:Xuni_Li/Sandbox_1/Initial2/1'>superimposed</scene> with CheA P3, P4, P5 (blue).
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On the right, is the CheW-CheA P4, P5 domain superimposed with CheW-CheA P3, P4, P5.
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Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation on specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>
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<scene name='User:Xuni_Li/Sandbox_1/Initial2/1'>Molecular Playground</scene>
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'''Prolyl hydroxylase domain (PHD) enzyme''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (EC 1.14.11.-)] is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of the specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>
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Molecular Playground banner: P4, P5 of CheA binding with CheW superimpose with P3, P4 P5 of CheA
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PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, these proteins are mostly found in the cytoplasm in contrast to [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally includes three [http://en.wiktionary.org/wiki/homolog homolog] members but was recently updated to include another member: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]), and a newly identified enzyme called P4H-TM (also recently named PHD4 and EGLN4). Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />
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<Structure load='Xuni1.pdb' size='300' frame='true' align='right' caption='P4, P5 of CheA binding with CheW (orange) superimpose with P3, P4, P5 of CheA (blue)' scene='User:Xuni_Li/Sandbox_1/Initial2/1' />
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[[Image:CheA.png]]
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<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>
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=== References ===
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Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.
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=== Structure ===
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PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Jelly_roll_fold/3'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases. Contained in this core are the three Fe(II)-binding ligands formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" />
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<references/>
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The <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Active_site/2'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the conserved two-histidine-one-carboxylate <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Fe_binding_triad_sequence/2'>triad</scene>, 2-OG and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />
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=Acknowledgement=
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=== Function ===
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To Luis E Ramirez-Tapia his advice to develop this page.
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The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens at position 4 of the residues Pro-402 and Pro-564 located in the C-terminal oxygen-dependent degradation domains (ODDs) of the [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
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The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
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=See Also=
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*tumor suppressor
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*[[Molecular Playground/Bacterial Chemotaxis Receptors]]
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*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
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*[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]
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*regulator of cell differentiation
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===3D structures of prolyl hydroxylase domain===
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[[Prolyl hydroxylase domain]]
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=== References ===
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<references/>
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Current revision

Cytoplasmic Domain of Thermotoga maritima receptor

Drag the structure with the mouse to rotate

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.

Contents

Introduction

Bacteria use their receptors to sense the environment to change their swimming patterns. There are different kinds of chemoreceptors that respond to different stimuli. The figure on the right is the methyl-accepting protein of Thermotoga maritima . Bacteria like to flee away from the repellent when high concentrations are present in the environment. CheA is a histidine kinase that associates with CheW, an adaptor protein, will cause the flagella to turn clockwise and result in a tumbling motion. On the other hand, when a high concentration of attractants are present in the environment, the CheA kinase will be turned off, cause flagella to turn counterclockwise, resulting in a forward swimming pattern. [1]

Image:Receptor.png

Structure and Functions

Chemoreceptors usually contain a periplasmic ligand binding domain, the transmembrane domain, a HAMP domain which is for signal conversion, and the cytoplasmic domain that contains the methylation sites, flexible bundle and protein binding sites where CheA and CheW bind. CheA is a histidine kinase that contains five units. The P1 domain is the site of substrate autophosphorylation that associates with kinase P4 domain, P2 is where phosphate transfers to CheY, another response regulator protein, from P1. P3, P4 and P5 are the dimerization, kinase and the receptor-coupling domains. The P3 domain was predicted to interact with CheW which stabilize the interface between P3 and P5. The NMR structure has shown that P5 is proximal to the CheW β barrel (residues 635-660). [2] On the right, is the CheW with CheA P4, P5 domains (orange) with CheA P3, P4, P5 (blue).


Molecular Playground banner: P4, P5 of CheA binding with CheW superimpose with P3, P4 P5 of CheA

P4, P5 of CheA binding with CheW (orange) superimpose with P3, P4, P5 of CheA (blue)

Drag the structure with the mouse to rotate

Image:CheA.png

References

  1. ↑ Hazelbauer, Falke and Parkinson. "Bacterial chemoreceptors: high-performance signaling in networked arrays." Biochemical Sciences, 2007, 33 (1), 9-19. PMID:[1]
  2. ↑ Park, Borbat, Gonzalez-Bonet, Bhatnagar, et al. "Reconstruction of the chemotaxis receptor-kinase assembly." Nature Structural and Molecular Biology, April 23, 2006, 13 (5), 400-407. PMID:[2]

Acknowledgement

To Luis E Ramirez-Tapia his advice to develop this page.

See Also

Proteopedia Page Contributors and Editors (what is this?)

Xuni Li

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