1zw7

From Proteopedia

(Difference between revisions)

Current revision

Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences

Structural highlights

1zw7 is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBI4P_YEAST 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, and DNA-damage responses. 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 (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

Single amino acid substitutions rarely produce substantial changes in protein structure. Here we show that substitution of the C-cap residue in the alpha-helix of ubiquitin with proline (34P variant) leads to dramatic structural changes. The resulting conformational perturbation extends over the last two turns of the alpha-helix and leads to enhanced flexibility for residues 27-37. Thermodynamic analysis of this ubiquitin variant using differential scanning calorimetry reveals that the thermal unfolding transition remains highly cooperative, exhibiting two-state behavior. Similarities with the wild type in the thermodynamic parameters (heat capacity change upon unfolding and m-value) of unfolding monitored by DSC and chemical denaturation suggests that the 34P variant has comparable buried surface area. The hydrophobic core of 34P variant is not packed as well as that of the wild type protein as manifested by a lower enthalpy of unfolding. The increased mobility of the polypeptide chain of this ubiquitin variant allows the transient opening of the hydrophobic core as evidenced by ANS binding. Taken together, these results suggest exceptional robustness of cooperativity in protein structures.

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.,Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI Biophys Chem. 2007 Mar;126(1-3):25-35. Epub 2006 Apr 5. PMID:16713063^[1]

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

References

↑ Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI. Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem. 2007 Mar;126(1-3):25-35. Epub 2006 Apr 5. PMID:16713063 doi:10.1016/j.bpc.2006.03.017

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/1zw7"

@@ Line 1: / Line 1: @@
 ==Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences==
-<StructureSection load='1zw7' size='340' side='right'caption='[[1zw7]], [[NMR_Ensembles_of_Models | 21 NMR models]]' scene=''>
+<StructureSection load='1zw7' size='340' side='right'caption='[[1zw7]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1zw7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZW7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1zw7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZW7 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBI1, RPL40A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1zw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zw7 OCA], [https://pdbe.org/1zw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zw7 RCSB], [https://www.ebi.ac.uk/pdbsum/1zw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zw7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBI4P_YEAST UBI4P_YEAST] 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, and DNA-damage responses. 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 (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Dangi, B]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Ermolenko, D N]]
+[[Category: Dangi B]]
-[[Category: Gronenborn, A M]]
+[[Category: Ermolenko DN]]
-[[Category: Makhatadze, G I]]
+[[Category: Gronenborn AM]]
-[[Category: Dynamic]]
+[[Category: Makhatadze GI]]
-[[Category: Structural protein]]
-[[Category: Thermodynamic]]

1zw7

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Current revision

Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences

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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