1dml

From Proteopedia

(Difference between revisions)

Revision as of 06:30, 11 August 2021

CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL

Structural highlights

1dml is a 8 chain structure with sequence from Hhv-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1plq, 1axc, 1b8h
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PAP_HHV11] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.^[1] [DPOL_HHV1A] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (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

Herpes simplex virus DNA polymerase is a heterodimer composed of a catalytic subunit, Pol, and an unusual processivity subunit, UL42, which, unlike processivity factors such as PCNA, directly binds DNA. The crystal structure of a complex of the C-terminal 36 residues of Pol bound to residues 1-319 of UL42 reveals remarkable similarities between UL42 and PCNA despite contrasting biochemical properties and lack of sequence homology. Moreover, the Pol-UL42 interaction resembles the interaction between the cell cycle regulator p21 and PCNA. The structure and previous data suggest that the UL42 monomer interacts with DNA quite differently than does multimeric toroidal PCNA. The details of the structure lead to a model for the mechanism of UL42, provide the basis for drug design, and allow modeling of other proteins that lack sequence homology with UL42 or PCNA.

The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.,Zuccola HJ, Filman DJ, Coen DM, Hogle JM Mol Cell. 2000 Feb;5(2):267-78. PMID:10882068^[2]

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

References

↑ Gottlieb J, Marcy AI, Coen DM, Challberg MD. The herpes simplex virus type 1 UL42 gene product: a subunit of DNA polymerase that functions to increase processivity. J Virol. 1990 Dec;64(12):5976-87. PMID:2173776
↑ Zuccola HJ, Filman DJ, Coen DM, Hogle JM. The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase. Mol Cell. 2000 Feb;5(2):267-78. PMID:10882068

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1dml' size='340' side='right'caption='[[1dml]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DML FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DML FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1plq|1plq]], [[1axc|1axc]], [[1b8h|1b8h]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1plq|1plq]], [[1axc|1axc]], [[1b8h|1b8h]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [http://pdbe.org/1dml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [http://www.ebi.ac.uk/pdbsum/1dml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dml OCA], [https://pdbe.org/1dml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dml RCSB], [https://www.ebi.ac.uk/pdbsum/1dml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dml ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref>  [[http://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).
+[[https://www.uniprot.org/uniprot/PAP_HHV11 PAP_HHV11]] Plays an essential role in viral DNA replication by acting as the polymerase accessory subunit. Associates with the viral polymerase to increase its processivity and forms high-affinity direct interactions with DNA. Facilitates the origin-binding protein UL9 loading onto DNA thus increasing its ability to assemble into a functional complex capable of unwinding duplex DNA.<ref>PMID:2173776</ref>  [[https://www.uniprot.org/uniprot/DPOL_HHV1A DPOL_HHV1A]] Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1dml

From Proteopedia

Revision as of 06:30, 11 August 2021

CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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