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2lj5

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Revision as of 19:18, 1 August 2018

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Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings

Structural highlights

2lj5 is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2kox
Gene:	UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Warning: this is a large structure, and loading might take a long time or not happen at all.

Function

[RL40_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] Ribosomal protein L40 is a component of the 60S subunit of the ribosome.^[3] ^[4]

Publication Abstract from PubMed

Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.,Montalvao RW, De Simone A, Vendruscolo M J Biomol NMR. 2012 Jun 23. PMID:22729708^[5]

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
↑ 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
↑ Montalvao RW, De Simone A, Vendruscolo M. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings. J Biomol NMR. 2012 Jun 23. PMID:22729708 doi:10.1007/s10858-012-9644-3

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2lj5"

Categories: Human | Montalvao, R | Simone, A De | Vendruscolo, M | Signaling protein

@@ Line 1: / Line 1: @@
+{{Large structure}}
 ==Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings==
 <StructureSection load='2lj5' size='340' side='right' caption='[[2lj5]], [[NMR_Ensembles_of_Models | 301 NMR models]]' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kox|2kox]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://pdbe.org/2lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum]</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=2lj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lj5 OCA], [http://pdbe.org/2lj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2lj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lj5 ProSAT]</span></td></tr>
 </table>
 {{Large structure}}

2lj5

From Proteopedia

Revision as of 19:18, 1 August 2018

Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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