This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2mbb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:30, 2 March 2023

Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex

Structural highlights

2mbb is a 2 chain structure with sequence from Homo sapiens and Streptococcus sp. 'group G'. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPG1_STRSG Binds to the constant Fc region of IgG with high affinity.POLI_HUMAN Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Unambiguous detection and assignment of intermolecular NOEs are essential for structure determination of protein complexes by NMR. Such information has traditionally been obtained with 3-D half-filtered experiments, where scalar coupling-based purging of intramolecular signals allows for selective detection of intermolecular NOEs. However, due to the large variation of (1)JHC scalar couplings and limited chemical shift dispersion in the indirect proton dimension, it is difficult to obtain reliable and complete assignments of interfacial NOEs. Here, we demonstrate a strategy that combines selective labeling and high-resolution 4-D NOE spectroscopy with sparse sampling for reliable identification and assignment of intermolecular NOEs. Spectral subtraction of component-labeled complexes from a uniformly-labeled protein complex yields an "omit" spectrum containing positive intermolecular NOEs with little signal degeneracy. Such a strategy can be broadly applied to unbiased detection, assignment and presentation of intermolecular NOEs of protein complexes.

Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes.,Wang S, Zhou P J Biomol NMR. 2014 Jun;59(2):51-6. doi: 10.1007/s10858-014-9834-2. Epub 2014 May , 1. PMID:24789524^[8]

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

References

↑ Tissier A, Frank EG, McDonald JP, Iwai S, Hanaoka F, Woodgate R. Misinsertion and bypass of thymine-thymine dimers by human DNA polymerase iota. EMBO J. 2000 Oct 2;19(19):5259-66. PMID:11013228 doi:http://dx.doi.org/10.1093/emboj/19.19.5259
↑ Bebenek K, Tissier A, Frank EG, McDonald JP, Prasad R, Wilson SH, Woodgate R, Kunkel TA. 5'-Deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro. Science. 2001 Mar 16;291(5511):2156-9. PMID:11251121 doi:http://dx.doi.org/10.1126/science.1058386
↑ Frank EG, Tissier A, McDonald JP, Rapic-Otrin V, Zeng X, Gearhart PJ, Woodgate R. Altered nucleotide misinsertion fidelity associated with poliota-dependent replication at the end of a DNA template. EMBO J. 2001 Jun 1;20(11):2914-22. PMID:11387224 doi:http://dx.doi.org/10.1093/emboj/20.11.2914
↑ Faili A, Aoufouchi S, Flatter E, Gueranger Q, Reynaud CA, Weill JC. Induction of somatic hypermutation in immunoglobulin genes is dependent on DNA polymerase iota. Nature. 2002 Oct 31;419(6910):944-7. PMID:12410315 doi:http://dx.doi.org/10.1038/nature01117
↑ Haracska L, Prakash L, Prakash S. A mechanism for the exclusion of low-fidelity human Y-family DNA polymerases from base excision repair. Genes Dev. 2003 Nov 15;17(22):2777-85. PMID:14630940 doi:10.1101/gad.1146103
↑ Washington MT, Minko IG, Johnson RE, Wolfle WT, Harris TM, Lloyd RS, Prakash S, Prakash L. Efficient and error-free replication past a minor-groove DNA adduct by the sequential action of human DNA polymerases iota and kappa. Mol Cell Biol. 2004 Jul;24(13):5687-93. PMID:15199127 doi:http://dx.doi.org/10.1128/MCB.24.13.5687-5693.2004
↑ Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature. 2004 Jul 15;430(6997):377-80. PMID:15254543 doi:10.1038/nature02692
↑ Wang S, Zhou P. Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes. J Biomol NMR. 2014 Jun;59(2):51-6. doi: 10.1007/s10858-014-9834-2. Epub 2014 May , 1. PMID:24789524 doi:http://dx.doi.org/10.1007/s10858-014-9834-2

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/2mbb"

Categories: Homo sapiens | Large Structures | Streptococcus sp. 'group G' | Wang S | Zhou P

@@ Line 1: / Line 1: @@
 ==Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex==
-<StructureSection load='2mbb' size='340' side='right'caption='[[2mbb]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2mbb' size='340' side='right'caption='[[2mbb]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2mbb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Strsg Strsg]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MBB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2mbb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Streptococcus_sp._'group_G' Streptococcus sp. 'group G']. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MBB FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</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=2mbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mbb OCA], [https://pdbe.org/2mbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mbb RCSB], [https://www.ebi.ac.uk/pdbsum/2mbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mbb 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=2mbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mbb OCA], [https://pdbe.org/2mbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mbb RCSB], [https://www.ebi.ac.uk/pdbsum/2mbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mbb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SPG1_STRSG SPG1_STRSG]] Binds to the constant Fc region of IgG with high affinity. [[https://www.uniprot.org/uniprot/UBB_HUMAN 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.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
+[https://www.uniprot.org/uniprot/SPG1_STRSG SPG1_STRSG] Binds to the constant Fc region of IgG with high affinity.[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Strsg]]
+[[Category: Streptococcus sp. 'group G']]
-[[Category: Wang, S]]
+[[Category: Wang S]]
-[[Category: Zhou, P]]
+[[Category: Zhou P]]
-[[Category: Polymerase iota]]
-[[Category: Signaling protein]]
-[[Category: Transferase]]
-[[Category: Ubiquitin]]
-[[Category: Ubm]]
-[[Category: Ubm1]]

2mbb

From Proteopedia

Revision as of 06:30, 2 March 2023

Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox