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The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.

Iyer LM, Burroughs AM, Aravind L.

Genome Biol. 2006;7(7):R60.PMID: 16859499 [PubMed - indexed for MEDLINE]Related articlesFree article

Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.

Iyer LM, Koonin EV, Aravind L.

Cell Cycle. 2004 Nov;3(11):1440-50. Epub 2004 Nov 6.PMID: 15483401 [PubMed - indexed for MEDLINE]Related articlesFree article

Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation.

Burroughs AM, Iyer LM, Aravind L.

Proteins. 2009 Jun;75(4):895-910.PMID: 19089947 [PubMed - indexed for MEDLINE]Related articles

Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.

Burroughs AM, Balaji S, Iyer LM, Aravind L.

Biol Direct. 2007 Jul 2;2:18.PMID: 17605815 [PubMed]Related articlesFree article

The NYN domains: novel predicted RNAses with a PIN domain-like fold.

Anantharaman V, Aravind L.

RNA Biol. 2006 Jan-Mar;3(1):18-27. Epub 2006 Jan 23.PMID: 17114934 [PubMed - indexed for MEDLINE]Related articlesFree article

Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.

Burroughs AM, Jaffee M, Iyer LM, Aravind L.

J Struct Biol. 2008 May;162(2):205-18. Epub 2008 Jan 1.PMID: 18276160 [PubMed - indexed for MEDLINE]Related articlesFree article

FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes.

Borziak K, Zhulin IB.

Bioinformatics. 2007 Oct 1;23(19):2518-21. Epub 2007 Sep 12.PMID: 17855421 [PubMed - indexed for MEDLINE]Related articlesFree article

A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination.

Brzovic PS, Lissounov A, Christensen DE, Hoyt DW, Klevit RE.

Mol Cell. 2006 Mar 17;21(6):873-80.PMID: 16543155 [PubMed - indexed for MEDLINE]Related articles

Ubiquitin C-terminal electrophiles are activity-based probes for identification and mechanistic study of ubiquitin conjugating machinery.

Love KR, Pandya RK, Spooner E, Ploegh HL.

ACS Chem Biol. 2009 Apr 17;4(4):275-87.PMID: 19256548 [PubMed - indexed for MEDLINE]Related articles

Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions.

Venancio TM, Balaji S, Iyer LM, Aravind L.

Genome Biol. 2009;10(3):R33. Epub 2009 Mar 30.PMID: 19331687 [PubMed - indexed for MEDLINE]Related articlesFree article

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.

Makarova KS, Wolf YI, van der Oost J, Koonin EV.

Biol Direct. 2009 Aug 25;4:29.PMID: 19706170 [PubMed - indexed for MEDLINE]Related articlesFree article

Specificity of the interaction between ubiquitin-associated domains and ubiquitin.

Mueller TD, Kamionka M, Feigon J.

J Biol Chem. 2004 Mar 19;279(12):11926-36. Epub 2004 Jan 5.PMID: 14707125 [PubMed - indexed for MEDLINE]Related articlesFree article

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.

Leipe DD, Koonin EV, Aravind L.

J Mol Biol. 2004 Oct 8;343(1):1-28. Review.PMID: 15381417 [PubMed - indexed for MEDLINE]Related articles

The basis for selective E1-E2 interactions in the ISG15 conjugation system.

Durfee LA, Kelley ML, Huibregtse JM.

J Biol Chem. 2008 Aug 29;283(35):23895-902. Epub 2008 Jun 26.PMID: 18583345 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif.

Bürglin TR.

BMC Genomics. 2008 Mar 11;9:127.PMID: 18334026 [PubMed - indexed for MEDLINE]Related articlesFree article

Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages.

Kim HT, Kim KP, Lledias F, Kisselev AF, Scaglione KM, Skowyra D, Gygi SP, Goldberg AL.

J Biol Chem. 2007 Jun 15;282(24):17375-86. Epub 2007 Apr 10.PMID: 17426036 [PubMed - indexed for MEDLINE]Related articlesFree article

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins.

Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L.

Mol Biosyst. 2009 Dec;5(12):1636-60. Epub 2009 Oct 13.PMID: 20023723 [PubMed - in process]Related articles

Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways.

Capili AD, Lima CD.

Curr Opin Struct Biol. 2007 Dec;17(6):726-35. Epub 2007 Oct 4. Review.PMID: 17919899 [PubMed - indexed for MEDLINE]Related articlesFree article

Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.

Hamilton KS, Ellison MJ, Barber KR, Williams RS, Huzil JT, McKenna S, Ptak C, Glover M, Shaw GS.

Structure. 2001 Oct;9(10):897-904.PMID: 11591345 [PubMed - indexed for MEDLINE]Related articles

The ligation systems for ubiquitin and ubiquitin-like proteins.

Tanaka K, Suzuki T, Chiba T.

Mol Cells. 1998 Oct 31;8(5):503-12. Review.PMID: 9856335 [PubMed - indexed for MEDLINE]Related articles