1nkk

From Proteopedia

(Difference between revisions)

Revision as of 08:52, 2 December 2020

COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR

Structural highlights

1nkk is a 8 chain structure with sequence from Hcmv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:	, , ,
Related:	2wpo, 1njt, 1nju, 1nkm
Gene:	UL80 OR APNG (HCMV)
Activity:	Assemblin, with EC number 3.4.21.97
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SCAF_HCMVA] Capsid scaffolding protein acts as a scaffold protein by binding major capsid protein UL86 in the cytoplasm, inducing the nuclear localization of both proteins. Multimerizes in the nucleus such as protein UL86 forms the icosahedral T=16 capsid. Autocatalytic cleavage releases the assembly protein, and subsequently abolishes interaction with major capsid protein UL86. Cleavages products are evicted from the capsid before or during DNA packaging (By similarity). Assemblin is a protease essential for virion assembly in the nucleus. Catalyzes the cleavage of the assembly protein after complete capsid formation. Assemblin and cleavages products are evicted from the capsid before or during DNA packaging (By similarity). Assembly protein plays a major role in capsid assembly. Acts as a scaffold protein by binding major capsid protein UL86. Multimerizes in the nucleus such as protein UL86 forms the icosahedral T=16 capsid. Cleaved by assemblin after capsid completion. The cleavages products are evicted from the capsid before or during DNA packaging (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Herpesvirus protease is required for the life cycle of the virus and is an attractive target for the design and development of new anti-herpes agents. The protease belongs to a new class of serine proteases, with a novel backbone fold and a unique Ser-His-His catalytic triad. Here we report the crystal structures of human cytomegalovirus protease in complex with two peptidomimetic inhibitors. The structures reveal a new hydrogen-bonding interaction between the main chain carbonyl of the P(5) residue and the main chain amide of amino acid 137 of the protease, which is important for the binding affinity of the inhibitor. Conformational flexibility was observed in the S(3) pocket of the enzyme, and this is supported by our characterization of several mutants in this pocket. One of the structures is at 2.5 A resolution, allowing us for the first time to locate ordered solvent molecules in the inhibitor complex. The presence of two solvent molecules in the active site may have implications for the design of new inhibitors against this enzyme. Favorable and stereospecific interactions have been established in the S(1)' pocket for one of these inhibitors.

Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease.,Khayat R, Batra R, Qian C, Halmos T, Bailey M, Tong L Biochemistry. 2003 Feb 4;42(4):885-91. PMID:12549906^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Khayat R, Batra R, Qian C, Halmos T, Bailey M, Tong L. Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease. Biochemistry. 2003 Feb 4;42(4):885-91. PMID:12549906 doi:10.1021/bi027045s

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nkk"

@@ Line 1: / Line 1: @@
 ==COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR==
-<StructureSection load='1nkk' size='340' side='right' caption='[[1nkk]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1nkk' size='340' side='right'caption='[[1nkk]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nkk]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hcmv Hcmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nkk]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hcmv Hcmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NKK FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CFT:TRIFLUOROMETHANE'>CFT</scene>, <scene name='pdbligand=DMH:N4,N4-DIMETHYL-ASPARAGINE'>DMH</scene>, <scene name='pdbligand=DMK:3,3-DIMETHYL+ASPARTIC+ACID'>DMK</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wpo|2wpo]], [[1njt|1njt]], [[1nju|1nju]], [[1nkm|1nkm]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wpo|2wpo]], [[1njt|1njt]], [[1nju|1nju]], [[1nkm|1nkm]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UL80 OR APNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10359 HCMV])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assemblin Assemblin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.97 3.4.21.97] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkk OCA], [http://pdbe.org/1nkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkk RCSB], [http://www.ebi.ac.uk/pdbsum/1nkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkk ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkk OCA], [http://pdbe.org/1nkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkk RCSB], [http://www.ebi.ac.uk/pdbsum/1nkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkk ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 31: / Line 31: @@
 </div>
 <div class="pdbe-citations 1nkk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Virus protease 3D structures|Virus protease 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 40: @@
 [[Category: Assemblin]]
 [[Category: Hcmv]]
+[[Category: Large Structures]]
 [[Category: Bailey, M]]
 [[Category: Batra, R]]

1nkk

From Proteopedia

Revision as of 08:52, 2 December 2020

COMPLEX STRUCTURE OF HCMV PROTEASE AND A PEPTIDOMIMETIC INHIBITOR

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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