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5dk8

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Revision as of 08:07, 8 April 2020

Human ubiquitin in the P1 space group

Structural highlights

5dk8 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	UBB (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[UBB_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.^[1] ^[2]

Publication Abstract from PubMed

Ubiquitin is a small globular protein that has a considerable number of lysine residues on its surface. This results in a high surface entropy that precludes the formation of crystal-packing interactions. To date, only a few structures of the native form of ubiquitin have been solved, and most of the crystals that led to these structures were obtained in the presence of different divalent metal cations. In this work, a new crystallographic structure of human ubiquitin solved from crystals grown in the presence of magnesium is presented. The crystals belonged to a triclinic space group, with unit-cell parameters a = 29.96, b = 30.18, c = 41.41 A, alpha = 88.52, beta = 79.12, gamma = 67.37 degrees . The crystal lattice is composed of stacked layers of human ubiquitin molecules with a large hydrophobic interface and a smaller polar interface in which the magnesium ion lies at the junction between adjacent layers in the crystal. The metal ion appears in a hexa-aquo coordination, which is key to facilitating the crystallization of the protein.

New crystal form of human ubiquitin in the presence of magnesium.,Camara-Artigas A, Plaza-Garrido M, Martinez-Rodriguez S, Bacarizo J Acta Crystallogr F Struct Biol Commun. 2016 Jan 1;72(Pt 1):29-35. doi:, 10.1107/S2053230X15023390. Epub 2016 Jan 1. PMID:26750481^[3]

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

References

↑ Huang F, Kirkpatrick D, Jiang X, Gygi S, Sorkin A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Mol Cell. 2006 Mar 17;21(6):737-48. PMID:16543144 doi:S1097-2765(06)00120-1
↑ Komander D. The emerging complexity of protein ubiquitination. Biochem Soc Trans. 2009 Oct;37(Pt 5):937-53. doi: 10.1042/BST0370937. PMID:19754430 doi:10.1042/BST0370937
↑ Camara-Artigas A, Plaza-Garrido M, Martinez-Rodriguez S, Bacarizo J. New crystal form of human ubiquitin in the presence of magnesium. Acta Crystallogr F Struct Biol Commun. 2016 Jan 1;72(Pt 1):29-35. doi:, 10.1107/S2053230X15023390. Epub 2016 Jan 1. PMID:26750481 doi:http://dx.doi.org/10.1107/S2053230X15023390

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5dk8"

Categories: Human | Large Structures | Bacarizo, J | Camara-Artigas, A | Signaling protein

@@ Line 1: / Line 1: @@
 ==Human ubiquitin in the P1 space group==
-<StructureSection load='5dk8' size='340' side='right' caption='[[5dk8]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
+<StructureSection load='5dk8' size='340' side='right'caption='[[5dk8]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dk8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DK8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dk8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DK8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DK8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dk8 OCA], [http://pdbe.org/5dk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dk8 RCSB], [http://www.ebi.ac.uk/pdbsum/5dk8 PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dk8 OCA], [http://pdbe.org/5dk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dk8 RCSB], [http://www.ebi.ac.uk/pdbsum/5dk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dk8 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 5dk8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin|Ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Bacarizo, J]]
 [[Category: Camara-Artigas, A]]
 [[Category: Signaling protein]]

5dk8

From Proteopedia

Revision as of 08:07, 8 April 2020

Human ubiquitin in the P1 space group

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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