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Farnesyl diphosphate synthase 3D structures

2021-04-18T21:45:21Z

Sandra B. Gabelli:

==3D structures of farnesyl diphosphate synthase==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*Farnesyl diphosphate synthase

**[[1zw5]], [[2f7m]], [[4xqr]], [[4xqs]], [[4xqt]] – hFPS – human 
**[[1fps]]– cFPS – chicken 
**[[1ubv]] – cFPS (mutant) 
**[[5hxn]] – z,z-FPS – tomato 
**[[5hxo]] – z,z-FPS (mutant) 
**[[1rtr]]– FPS – ''Staphylococcus aureus'' 
**[[1yhk]], [[5qqc]], [[6r04]], [[3iba]], [[3icz]], [[3icm]], [[3icn]], [[1yhl]] – TcFPPS – ''Trypanosoma cruzi'' 
**[[6vjc]], [[6w71]], [[4k10]], [[4jzb]], [[4jzx]]– LmFPPS – ''Leishmania major'' 
**[[3lvs]], [[3m0g]] – FPS – ''Rhodobacter capsulatus'' 
**[[3m9u]] – LbFPS – ''Lactobacillus brevis'' 
**[[5ayp]] – FPS – ''Geobacillus stearothermophilus'' 

*FPS binary complexes

**[[1yq7]], [[1yv5]], [[2f89]], [[2f8c]], [[2f92]], [[2f94]], [[2f9k]], [[2rah]], [[2opn]], [[2vf6]], [[3b7l]], [[2opm]], [[3n1v]], [[3n1w]], [[3n3l]], [[3n45]], [[3n46]], [[3n49]], [[3n5j]], [[3n6k]], [[3n5h]], [[4dem]], [[4ga3]], [[4jvj]], [[4pvx]], [[4pvy]], [[4rxa]], [[5dgn]], [[5diq]], [[5djp]], [[5djr]], [[5djv]], [[5juz]], [[5jv0]], [[5jv1]], [[5jv2]], [[5ksx]], [[5ygi]], [[6n7y]], [[6n7z]], [[6n82]], [[6n83]], [[6oag]], [[6oah]] - hFPS + inhibitor 
**[[2qis]], [[3cp6]], [[3rye]], [[3s4j]], [[4n9u]] - hFPS (mutant) + inhibitor 
**[[4kfa]], [[4kpj]], [[4kq5]] - hFPS (mutant) + osteoporosis drug 
**[[4lpg]], [[4lph]], [[4n1z]], [[4p0x]] - hFPS + drug 
**[[4nfi]], [[4nfj]], [[4nfk]], [[4qxs]], [[4qpf]], [[5cg5]] - hFPS + bisphosphonate 
**[[4ng6]], [[4nke]], [[4nkf]], [[4nua]], [[4ogu]], [[4q23]] - hFPS (mutant) + bisphosphonate 
**[[5dgm]], [[5dgs]] - hFPS + monophosphonate 
**[[5ja0]] - hFPS + FPP 
**[[1ubw]], [[1ubx]] - cFPS (mutant) + GDP 
**[[1uby]] - cFPS (mutant) + dimethylallyl PP 
**[[6b07]], [[6b02]], [[6b04]], [[6b06]] – FPS + inhibitor – spruce budworm moth 
**[[5hxp]] – z,z-FPS (mutant) + IPP 
**[[5hxq]] – z,z-FPS (mutant) + DMSPP 
**[[2i19]], [[2ewg]], [[2ogd]], [[2p1c]], [[3dyg]], [[3dyh]], [[3efq]], [[3egt]] - TbFPS + inhibitor – ''Trypanosoma brucei'' 
**[[2for]]– FPS + IPP – ''Shigella flexneri'' 
**[[4jzb]], [[4jzx]], [[4k10]] – Leshmaniasis major FPS + inhibitor 
**[[3id0]], [[3iba]], [[3ick]], [[3icm]], [[3icn]], [[3icz]], [[5qpd]] – TcFPS + inhibitor 
**[[5qpe]], [[5qpk]], [[5qpo]], [[5qq3]], [[5qq8]] – TcFPS + imidazole inhibitor 
**[[5qpg]], [[5qpn]], [[6r08]] – TcFPS + indole inhibitor 
**[[5qpf]], [[5qq1]], [[6r09]], [[6r0a]], [[6r0b]] – TcFPS + piperazine inhibitor 
**[[6r06]] – TcFPS + piperidine inhibitor 
**[[5qph]], [[5qq0]] – TcFPS + morpholine inhibitor 
**[[5qpi]], [[5qpw]], [[5qpy]], [[5qq5]], [[5qqa]] – TcFPS + pyrazole inhibitor 
**[[5qps]] – TcFPS + oxazole inhibitor 
**[[5qpj]], [[5qpu]], [[5qq9]] – TcFPS + acetamide inhibitor 
**[[5qpq]] – TcFPS + ethanamide inhibitor 
**[[5qpv]] – TcFPS + caboxamide inhibitor 
**[[5qpl]], [[5qpm]], [[5qpp]], [[5qpr]], [[5qpz]], [[5qq4]] – TcFPS + urea inhibitor 
**[[5qpt]] – TcFPS + thiazine inhibitor 
**[[5qq2]], [[6r07]] – TcFPS + thiophene inhibitor 
**[[5qpx]] – TcFPS + quinoline inhibitor 
**[[5qq6]], [[5qq7]] – TcFPS + pyrrolidine inhibitor 
**[[6r05]] – TcFPS + pyridine inhibitor 
**[[5qqb]] – TcFPS + benzodiazo inhibitor 
**[[3pde]] – LbFPS + IPP 

*FPS ternary complexes

**[[2f8z]], [[4h5e]] - hFPS + IPP + inhibitor 
**[[4kpd]], [[4kqs]], [[4kqu]] - hFPS (mutant) + IPP + osteoporosis drug 
**[[4p0v]], [[4p0w]] - hFPS + 2 drugs 
**[[4h5c]], [[4h3c]], [[4h5d]], [[4lfv]] - hFPS + phosphate + inhibitor 
**[[5cg6]] - hFPS + IPP + bisphosphonate 
**[[4l2x]] - hFPS + PP + inhibitor 
**[[5hxt]] – z,z-FPS (mutant) + DMSPP + IPP 
**[[1rqi]] – EcFPS + IPP + dimethylallyl S-thioloPP – ''Escherichia coli'' 
**[[1rqj]] - EcFPS + IPP + inhibitor 
**[[1yhl]] – TcFPS + dimethylallyl PP + inhibitor 
**[[1yhm]], [[3iba]], [[3ick]], [[3icm]], [[3icn]], [[3icz]], [[4dwb]], [[4dwg]], [[4dxj]], [[4dzw]], [[4e1e]] - TcFPS + IPP + inhibitor 
**[[3ez3]] - PvFPS + IPP + inhibitor – ''Plasmodium vivax'' 
**[[3dyf]] - TbFPS + IPP + inhibitor 

}}

[[Category:Topic Page]]

Farnesyl diphosphate synthase 3D structures

2021-04-18T21:41:56Z

Sandra B. Gabelli:

==3D structures of farnesyl diphosphate synthase==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*Farnesyl diphosphate synthase

**[[1zw5]], [[2f7m]], [[4xqr]], [[4xqs]], [[4xqt]] – hFPS – human 
**[[1fps]]– cFPS – chicken 
**[[1ubv]] – cFPS (mutant) 
**[[5hxn]] – z,z-FPS – tomato 
**[[5hxo]] – z,z-FPS (mutant) 
**[[1rtr]]– FPS – ''Staphylococcus aureus'' 
**[[1yhk]], [[5qqc]], [[6r04]] – TcFPPS – ''Trypanosoma cruzi'' 
**[[6vjc]], [[6w71]], [[4k10]], [[4jzb]]– LmFPPS – ''Leishmania major'' 
**[[3lvs]], [[3m0g]] – FPS – ''Rhodobacter capsulatus'' 
**[[3m9u]] – LbFPS – ''Lactobacillus brevis'' 
**[[5ayp]] – FPS – ''Geobacillus stearothermophilus'' 

*FPS binary complexes

**[[1yq7]], [[1yv5]], [[2f89]], [[2f8c]], [[2f92]], [[2f94]], [[2f9k]], [[2rah]], [[2opn]], [[2vf6]], [[3b7l]], [[2opm]], [[3n1v]], [[3n1w]], [[3n3l]], [[3n45]], [[3n46]], [[3n49]], [[3n5j]], [[3n6k]], [[3n5h]], [[4dem]], [[4ga3]], [[4jvj]], [[4pvx]], [[4pvy]], [[4rxa]], [[5dgn]], [[5diq]], [[5djp]], [[5djr]], [[5djv]], [[5juz]], [[5jv0]], [[5jv1]], [[5jv2]], [[5ksx]], [[5ygi]], [[6n7y]], [[6n7z]], [[6n82]], [[6n83]], [[6oag]], [[6oah]] - hFPS + inhibitor 
**[[2qis]], [[3cp6]], [[3rye]], [[3s4j]], [[4n9u]] - hFPS (mutant) + inhibitor 
**[[4kfa]], [[4kpj]], [[4kq5]] - hFPS (mutant) + osteoporosis drug 
**[[4lpg]], [[4lph]], [[4n1z]], [[4p0x]] - hFPS + drug 
**[[4nfi]], [[4nfj]], [[4nfk]], [[4qxs]], [[4qpf]], [[5cg5]] - hFPS + bisphosphonate 
**[[4ng6]], [[4nke]], [[4nkf]], [[4nua]], [[4ogu]], [[4q23]] - hFPS (mutant) + bisphosphonate 
**[[5dgm]], [[5dgs]] - hFPS + monophosphonate 
**[[5ja0]] - hFPS + FPP 
**[[1ubw]], [[1ubx]] - cFPS (mutant) + GDP 
**[[1uby]] - cFPS (mutant) + dimethylallyl PP 
**[[6b07]], [[6b02]], [[6b04]], [[6b06]] – FPS + inhibitor – spruce budworm moth 
**[[5hxp]] – z,z-FPS (mutant) + IPP 
**[[5hxq]] – z,z-FPS (mutant) + DMSPP 
**[[2i19]], [[2ewg]], [[2ogd]], [[2p1c]], [[3dyg]], [[3dyh]], [[3efq]], [[3egt]] - TbFPS + inhibitor – ''Trypanosoma brucei'' 
**[[2for]]– FPS + IPP – ''Shigella flexneri'' 
**[[4jzb]], [[4jzx]], [[4k10]] – Leshmaniasis major FPS + inhibitor 
**[[3id0]], [[3iba]], [[3ick]], [[3icm]], [[3icn]], [[3icz]], [[5qpd]] – TcFPS + inhibitor 
**[[5qpe]], [[5qpk]], [[5qpo]], [[5qq3]], [[5qq8]] – TcFPS + imidazole inhibitor 
**[[5qpg]], [[5qpn]], [[6r08]] – TcFPS + indole inhibitor 
**[[5qpf]], [[5qq1]], [[6r09]], [[6r0a]], [[6r0b]] – TcFPS + piperazine inhibitor 
**[[6r06]] – TcFPS + piperidine inhibitor 
**[[5qph]], [[5qq0]] – TcFPS + morpholine inhibitor 
**[[5qpi]], [[5qpw]], [[5qpy]], [[5qq5]], [[5qqa]] – TcFPS + pyrazole inhibitor 
**[[5qps]] – TcFPS + oxazole inhibitor 
**[[5qpj]], [[5qpu]], [[5qq9]] – TcFPS + acetamide inhibitor 
**[[5qpq]] – TcFPS + ethanamide inhibitor 
**[[5qpv]] – TcFPS + caboxamide inhibitor 
**[[5qpl]], [[5qpm]], [[5qpp]], [[5qpr]], [[5qpz]], [[5qq4]] – TcFPS + urea inhibitor 
**[[5qpt]] – TcFPS + thiazine inhibitor 
**[[5qq2]], [[6r07]] – TcFPS + thiophene inhibitor 
**[[5qpx]] – TcFPS + quinoline inhibitor 
**[[5qq6]], [[5qq7]] – TcFPS + pyrrolidine inhibitor 
**[[6r05]] – TcFPS + pyridine inhibitor 
**[[5qqb]] – TcFPS + benzodiazo inhibitor 
**[[3pde]] – LbFPS + IPP 

*FPS ternary complexes

**[[2f8z]], [[4h5e]] - hFPS + IPP + inhibitor 
**[[4kpd]], [[4kqs]], [[4kqu]] - hFPS (mutant) + IPP + osteoporosis drug 
**[[4p0v]], [[4p0w]] - hFPS + 2 drugs 
**[[4h5c]], [[4h3c]], [[4h5d]], [[4lfv]] - hFPS + phosphate + inhibitor 
**[[5cg6]] - hFPS + IPP + bisphosphonate 
**[[4l2x]] - hFPS + PP + inhibitor 
**[[5hxt]] – z,z-FPS (mutant) + DMSPP + IPP 
**[[1rqi]] – EcFPS + IPP + dimethylallyl S-thioloPP – ''Escherichia coli'' 
**[[1rqj]] - EcFPS + IPP + inhibitor 
**[[1yhl]] – TcFPS + dimethylallyl PP + inhibitor 
**[[1yhm]], [[3iba]], [[3ick]], [[3icm]], [[3icn]], [[3icz]], [[4dwb]], [[4dwg]], [[4dxj]], [[4dzw]], [[4e1e]] - TcFPS + IPP + inhibitor 
**[[3ez3]] - PvFPS + IPP + inhibitor – ''Plasmodium vivax'' 
**[[3dyf]] - TbFPS + IPP + inhibitor 

}}

[[Category:Topic Page]]

Major Histocompatibility Complex Class I

2021-03-18T22:26:27Z

Sandra B. Gabelli:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts. As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major histocompatibility complex

2020-07-27T17:43:58Z

Sandra B. Gabelli:

<StructureSection load='' size='350' side='right' caption='Human MHC class I antigen (cyan) with β 2-microglobulin (green) and peptide from Hepatitis virus (deeppink) [[3ox8]]' scene='45/457390/Cv/1'>
__TOC__
== Function ==
''' Major Histocompatibility Complex''' (MHC) molecules bind peptides derived from degraded proteins and present these peptides on the surface of the cell. Cytotoxic T-lymphocytes or helper T cells recognize the MHC:peptide complex on the surface of the cell and, if the presented peptide (antigen) is suggestive of a pathogenic or foreign protein, trigger an immune response. In this way, MHC molecules allow for immune system detection of cellular activity, making them an essential part of the organism’s immune system. MHC molecules are divided into Class I and Class II molecules based on the types of cells that typically express them and the types of peptides they typically bind.
 
* '''MHC class I''' ([[Major Histocompatibility Complex Class I]]) are found in all nucleated cells and platelets. These cell surface proteins display peptides from cellular intrinsic proteins<ref>PMID:18675588</ref><ref> DOI: 10.1074/jbc.RA119.010251 </ref>. For more details see 
**[[Effect of HCMV on Major Histocompatibility Complex Class I]] 
**[[MR1 Binds Vitamin Metabolites]]. 
* '''MHC class II''' are found in professional antigen-presenting cells like macrophages. These cell surface proteins display peptides from cellular extrinsic proteins<ref>PMID:15120183</ref>. 
For information on MHC class II interactions with T-cell receptor and gliadin peptide see [[SP3.4-TCR-HLA-DQ8-α-1-gliadin complex]].

== Structural highlights ==
Both Class I and Class II MHC molecules are heterodimers with two extracellular subunits (α and β) and one or two transmembrane helices that extend from the extracellular subunits to the cytoplasm. In Class I molecules, the α subunit is divided into three domains (α1, α2, and α3). The α1 and α2 domains together form an eight strand β-sheet platform and two α-helix rails that serve as the peptide-binding groove. The α3 domain forms an immunoglobulin-like fold that carries the peptide-binding groove with added support from with the β subunit (a β2-microglobulin molecule encoded outside of the MHC Class I gene locus). In Class II molecules, both the α and β subunits are divided into two domains (α1, α2,β1, and β2). The peptide-binding groove is formed by the α1 and β1 domains. The α2 and β2 domains carry the peptide-binding groove. Unlike the β subunits of Class I molecules, the β subunits of Class II molecules are encoded within the MHC Class II gene. While the α subunit is polymorphic for both MHC Classes, the β subunit is polymorphic only for Class II molecules.
<scene name='45/457390/Cv/5'>Human MHC class I antigen with β 2-microglobulin and peptide from Hepatitis virus</scene>.
The <scene name='45/457390/Cv/6'>peptide derived from Hepatitis virus binds MHC in a peptide-recognition groove and makes various interactions with side chains and with water molecules</scene><ref>PMID:21538979</ref>. Water molecules shown as red spheres.

==List of Published 3D Structures of MHC==
[[MHC 3D structures of MHC]]
</StructureSection>

==See Also==
* [[Major Histocompatibility Complex Class I]] which is about the history and impact of the first crystal structure.
* A narrated YouTube video tutorial on MHC I and II (25 min) available at [http://molviz.org MolviZ.Org]
* [[Highest impact structures]]: 1987.

== References ==
<references/>

[[Category:Topic Page]]

Major histocompatibility complex

2020-07-27T17:41:39Z

Sandra B. Gabelli:

<StructureSection load='' size='350' side='right' caption='Human MHC class I antigen (cyan) with β 2-microglobulin (green) and peptide from Hepatitis virus (deeppink) [[3ox8]]' scene='45/457390/Cv/1'>
__TOC__
== Function ==
''' Major Histocompatibility Complex''' (MHC) molecules bind peptides derived from degraded proteins and present these peptides on the surface of the cell. Cytotoxic T-lymphocytes or helper T cells recognize the MHC:peptide complex on the surface of the cell and, if the presented peptide (antigen) is suggestive of a pathogenic or foreign protein, trigger an immune response. In this way, MHC molecules allow for immune system detection of cellular activity, making them an essential part of the organism’s immune system. MHC molecules are divided into Class I and Class II molecules based on the types of cells that typically express them and the types of peptides they typically bind.
 
* '''MHC class I''' ([[Major Histocompatibility Complex Class I]]) are found in all nucleated cells and platelets. These cell surface proteins display peptides from cellular intrinsic proteins<ref>PMID:18675588</ref>. For more details see 
**[[Effect of HCMV on Major Histocompatibility Complex Class I]] 
**[[MR1 Binds Vitamin Metabolites]]. 
* '''MHC class II''' are found in professional antigen-presenting cells like macrophages. These cell surface proteins display peptides from cellular extrinsic proteins<ref>PMID:15120183</ref>. 
For information on MHC class II interactions with T-cell receptor and gliadin peptide see [[SP3.4-TCR-HLA-DQ8-α-1-gliadin complex]].

== Structural highlights ==
Both Class I and Class II MHC molecules are heterodimers with two extracellular subunits (α and β) and one or two transmembrane helices that extend from the extracellular subunits to the cytoplasm. In Class I molecules, the α subunit is divided into three domains (α1, α2, and α3). The α1 and α2 domains together form an eight strand β-sheet platform and two α-helix rails that serve as the peptide-binding groove. The α3 domain forms an immunoglobulin-like fold that carries the peptide-binding groove with added support from with the β subunit (a β2-microglobulin molecule encoded outside of the MHC Class I gene locus). In Class II molecules, both the α and β subunits are divided into two domains (α1, α2,β1, and β2). The peptide-binding groove is formed by the α1 and β1 domains. The α2 and β2 domains carry the peptide-binding groove. Unlike the β subunits of Class I molecules, the β subunits of Class II molecules are encoded within the MHC Class II gene. While the α subunit is polymorphic for both MHC Classes, the β subunit is polymorphic only for Class II molecules.
<scene name='45/457390/Cv/5'>Human MHC class I antigen with β 2-microglobulin and peptide from Hepatitis virus</scene>.
The <scene name='45/457390/Cv/6'>peptide derived from Hepatitis virus binds MHC in a peptide-recognition groove and makes various interactions with side chains and with water molecules</scene><ref>PMID:21538979</ref>. Water molecules shown as red spheres.

==List of Published 3D Structures of MHC==
[[MHC 3D structures of MHC]]
</StructureSection>

==See Also==
* [[Major Histocompatibility Complex Class I]] which is about the history and impact of the first crystal structure.
* A narrated YouTube video tutorial on MHC I and II (25 min) available at [http://molviz.org MolviZ.Org]
* [[Highest impact structures]]: 1987.

== References ==
<references/>
<ref> DOI: 10.1074/jbc.RA119.010251 </ref>

[[Category:Topic Page]]

NudT16

2020-07-27T17:36:21Z

Sandra B. Gabelli:

<StructureSection load='6B09' size='350' side='right' caption='Crystal structure of HsNUDT16 in complex with diADPR, one monomer is shown in cyan with amino acids 4-17 in blue, the other monomer is shown in purple and has residues 3-17 colored in pink. (PDB entry [[6B09]])' scene='84/849734/Nudt16/5'>
__TOC__
==Introduction==
NudT16 is an archetypical member of the Nudix superfamily of hydrolases. Nudix hydrolases have in common a stretch of 23 amino acids called the Nudix signature sequence which is the binding site for the metal involved in diphosphate hydrolysis. Nudix hydrolases prefer substrates of the form NUcleoside, DIphosphate and X, hence their name NUDIX. Examples of such substrates are ATP where X is PPI, ADPribose where X is phospho-ribose or m7GTP-RNA where X is phospho-RNA. Their catalytic activity breakshydrolyze a phosphorus-oxygen bond resulting in a nucleoside monophosphate (NMP) and a phosphate linked to moiety X. While NudT16 was initially described as a nuclear RNA and cytoplasmic mRNA decapping enzyme, further studies have shown that it also effectively hydrolyzes inosine diphosphate (IDP) and its hazardous deoxyribose cognate (dIDP) into inosine monophosphate (IMP) and deoxy inosine monophosphate (dIMP), respectively <ref>PMID: 26121039</ref>. NudT16 was shown to hydrolyze ADPribose and polyADPr <ref>PMID: 30976021</ref>. Physiologically, NudT16 has been shown to regulate levels of 53BP1, an adaptor protein that recruits other proteins to the site of a DNA breakage, through hydrolytic removal of ADP-ribose (ADPr) from Poly-ADP-ribosylated 53BP1 <ref>PMID: 31911551</ref>.

==Structure==
[[Image:Figure1-Nudixsequence-NUDT16-01.png|400x450px]]
NudT16 is a homodimer. The ribbon diagram shows Nudt16’s structure with A structure on the right shows the enzyme (one monomer in cyan and the other in purple) in complex with diADPr. This dimerization allows for each subunit to have a deeper ADPr binding pocket. Each monomer consists of a two beta-sheets surrounded by alpha-helices, as per the canonical canonical NNudix fold, an a/b fold of two . One beta-sheets sandwiched by a-helices. is composed entirely of antiparallel strands, while the other has two central parallel strands sandwiched between two outer anti-parallel strands. The catalytically relevant Nudix signature characteristic of Nudix hydrolases consists of 23 highly conserved residues (G1Z2-6E7Z8-14R15E16U17Z18E19E20Z21G22U23, where Z is any amino acid and U is an aliphatic and hydrophobic residue) in a loop-helix-loop region. The residues of the Nudix signature sequence in NudT16 (GARRLELGEALALGSGWRHVCHA) are shown in light pink and dark blue. The Glu residues in the Nudix box play a role in metal ion chelation essential to substrate binding and in the deprotonation of a water molecule to form a hydroxide nucleophile. <ref>PMID: 26121039</ref> In contrast to the negatively charged pockets where metal ligands chelate, the adenosine binding pocket is positively charged. The mouth of the binding site is about 9 Å in width. Contrary to Nudix ADPRases,<ref> https://doi.org/10.1021/bi0259296</ref> <ref> PMID: 11323725</ref> Homo sapiens NudT16 (HsNudT16) binds adenosine of ADPr and buries it deep in the core, while leaving the non-adenosine ribose exposed to the surface. This orientation allows the exposed ribose to conjugate another protein. Many residues in the mouth of this binding pocket are also involved in hydrogen bonding, the binding of metal ligands, and serve to delimit the binding site.

== Biological Function ==
Although initially it was postulated that HsNudT16 biological function was to decapp mRNA, the work of Gong and co-workers shows that HsNudT16 removes the posttranslational modification ADP-ribosylation of 53BP1 and so it regulates 53BP1 levels<ref> doi: 10.1158/0008-5472.CAN-19-2205</ref>.

Interestingly, Thirawatananond et. al. investigated whether the widening of the ADPr binding site would allow for increased hydrolysis activity by NudT16. Nudt16 mutants F36A, F61S, and a double mutant with both F36A and F61S have NudT16 hydrolysis activity decreased in free ADPr, and it remained comparably efficient in mono(ADP-ribosylated) proteins, and increased in poly(ADP-ribosylated) proteins. <ref>PMID: 30976021</ref>

Iyama et. al. determined that NudT16 is a (Deoxy)inosine diphosphatase and that the loss of this protein is followed by increased accumulation of single-strand breaks in DNA, reduced proliferation, and increased cell arrest. They also found increased levels of inosine in RNA, which informed the conclusion that HsNudT16 functions in the nucleus to protect the cell from ITP and its detrimental effects <ref>PMID:20385596</ref> .

== Relevance ==

== References ==
<references/>

Farnesyl diphosphate synthase

2020-07-27T17:30:08Z

Sandra B. Gabelli:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
'''Farnesyl pyrophospate synthase''' (FPPS), also named '''Farnesyl diphosphate synthase''' (FPS), is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophospate (FPP).<ref>PMID:11152452</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

WWP2

2020-06-24T17:29:01Z

Sandra B. Gabelli:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation.
</StructureSection>
== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include Smads, Oct4, EGR2, and TIRF.

== References ==
<references/>
1. Chen, W.; Jiang, X.; Luo, Z. WWP2: A Multifunctional Ubiquitin Ligase Gene. Pathol. Oncol. Res. 2014, 20 (4), 799–803. doi:10.1007/s12253-014-9838-y.

2. Chen, Z., Jiang, H., Xu, W., Li, X., Dempsey, D. R., Zhang, X., . . . Cole, P. A. (2017). A Tunable Brake for HECT Ubiquitin Ligases. Molecular Cell, 66(3), 345-357. doi:10.1016/j.molcel.2017.03.020 PMID:28475870

3. Ingham, R.J., Gish, G., & Pawson, T.(2004) The Nedd4 family of E3 ubiquitin ligases: Functional diversity within a common modular architecture. Oncogene, 23(11), 1972-1984. doi:10.1038/sj.onc.1207436

WWP2

2020-06-24T17:27:00Z

Sandra B. Gabelli:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation.
</StructureSection>
== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include Smads, Oct4, EGR2, and TIRF.

== References ==
<references/>
1. Chen, W.; Jiang, X.; Luo, Z. WWP2: A Multifunctional Ubiquitin Ligase Gene. Pathol. Oncol. Res. 2014, 20 (4), 799–803. doi:10.1007/s12253-014-9838-y.

2. Chen, Z., Jiang, H., Xu, W., Li, X., Dempsey, D. R., Zhang, X., . . . Cole, P. A. (2017). A Tunable Brake for HECT Ubiquitin Ligases. Molecular Cell, 66(3), 345-357. doi:10.1016/j.molcel.2017.03.020 PMID:28475870

3. Ingham, R.J., Gish, G., & Pawson, T.(2004) The Nedd4 family of E3 ubiquitin ligases: Functional diversity within a common modular architecture. Oncogene, 23(11), 1972-1984. doi:10.1038/sj.onc.1207436

WWP2

2020-06-24T17:24:20Z

Sandra B. Gabelli:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/13">
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation.
</StructureSection>
== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include Smads, Oct4, EGR2, and TIRF.

== References ==
<references/>
1. Chen, W.; Jiang, X.; Luo, Z. WWP2: A Multifunctional Ubiquitin Ligase Gene. Pathol. Oncol. Res. 2014, 20 (4), 799–803. doi:10.1007/s12253-014-9838-y.

2. Chen, Z., Jiang, H., Xu, W., Li, X., Dempsey, D. R., Zhang, X., . . . Cole, P. A. (2017). A Tunable Brake for HECT Ubiquitin Ligases. Molecular Cell, 66(3), 345-357. doi:10.1016/j.molcel.2017.03.020 PMID:28475870

3. Ingham, R.J., Gish, G., & Pawson, T.(2004) The Nedd4 family of E3 ubiquitin ligases: Functional diversity within a common modular architecture. Oncogene, 23(11), 1972-1984. doi:10.1038/sj.onc.1207436

WWP2

2020-06-24T17:22:57Z

Sandra B. Gabelli:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/13">
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. A <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation.
</StructureSection>
== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include Smads, Oct4, EGR2, and TIRF.

== References ==
<references/>
1. Chen, W.; Jiang, X.; Luo, Z. WWP2: A Multifunctional Ubiquitin Ligase Gene. Pathol. Oncol. Res. 2014, 20 (4), 799–803. doi:10.1007/s12253-014-9838-y.

2. Chen, Z., Jiang, H., Xu, W., Li, X., Dempsey, D. R., Zhang, X., . . . Cole, P. A. (2017). A Tunable Brake for HECT Ubiquitin Ligases. Molecular Cell, 66(3), 345-357. doi:10.1016/j.molcel.2017.03.020 PMID:28475870

3. Ingham, R.J., Gish, G., & Pawson, T.(2004) The Nedd4 family of E3 ubiquitin ligases: Functional diversity within a common modular architecture. Oncogene, 23(11), 1972-1984. doi:10.1038/sj.onc.1207436

User:Sandra B. Gabelli

2020-06-24T17:19:47Z

Sandra B. Gabelli:

* Full Real Name: Sandra B. Gabelli

* Position: Associate Professor

* Institution (NO ABBREVIATIONS): Johns Hopkins University - School of Medicine - Department of Medicine

* City, State/Province, Country: Baltimore MD USA

* Field of Expertise or Study: structural biology, drug discovery, lipid kinases, PI3K pathway, nudix enzymes, FPPS, voltage gated sodium channel