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All change: protein conformation and the ubiquitination reaction cascade.

Riedinger C, Endicott JA - F1000 Biol Rep (2009)

Bottom Line: The structures of enzymes that collectively modify proteins by covalent addition of ubiquitin-like protein moieties have provided significant insights into the regulatory pathways they compose and have highlighted the importance of protein flexibility for the mechanism and regulation of the ubiquitination reaction.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biophysics and Department of Biochemistry South Parks Road, Oxford OX1 3QU UK.

ABSTRACT
The structures of enzymes that collectively modify proteins by covalent addition of ubiquitin-like protein moieties have provided significant insights into the regulatory pathways they compose and have highlighted the importance of protein flexibility for the mechanism and regulation of the ubiquitination reaction.

No MeSH data available.


Related in: MedlinePlus

Conformational change accompanies catalysis in E1s(a) A conformational switch accompanies double-loading of an E1. A comparison of the structure of a singly loaded E1 complex (APPBP1-UBA3-NEDD8-ATP, PDB code 1R4N [11], left-hand side) and that of the doubly loaded complex (PDB code 2NVU [8], right-hand side) elegantly demonstrates the conformational switch within the E1 that accompanies double-loading of the E1 with its cognate Ubl. The direction of the rearrangement of the UFD domain of UBA3 (that binds to the E2) as well as that in which the NEDD8 is passed on from the A site to the T site are indicated with arrows. The molecular surfaces of APPBP1 and UBA3 are highlighted in light cyan and grey, respectively. In the right-hand panel, the E2 Ubc12 is represented in turquoise. The UBA3 UFD domain (black) is shown in ribbon representation. Bound NEDD8 molecules are coloured red (A site) and orange (T site). (b) Comparison of singly charged E1 structures. Left panel: Uba1-Ub complex (PDB code 3CMM [10]). Right panel: APPBP1-UBA3-NEDD8-ATP complex. The bound small ubiquitin-like protein (Ub or NEDD8, respectively) is coloured red and the UFD domains of both E1 enzymes are coloured black. Within the E1 structures, the two juxtaposed catalytic cysteine half domains that compose the catalytic cysteine domain [19] are coloured pale yellow and light blue (respectively), the crossover loop that connects the adenylation and catalytic cysteine domains is coloured dark blue, and the molecular surface of the rest of the E1 is coloured grey (Uba1 and UBA3) and light cyan (APPBP1). A, adenylation; APPBP1, amyloid beta precursor protein-binding protein 1; NEDD8, neural precursor cell expressed, developmentally downregulated 8; PDB, Protein Data Bank; T, thioester; Ub, ubiquitin; Ubl, small ubiquitin-like protein; UBA3, ubiquitin-activating enzyme 3; UFD, ubiquitin-fold domain.
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fig-001: Conformational change accompanies catalysis in E1s(a) A conformational switch accompanies double-loading of an E1. A comparison of the structure of a singly loaded E1 complex (APPBP1-UBA3-NEDD8-ATP, PDB code 1R4N [11], left-hand side) and that of the doubly loaded complex (PDB code 2NVU [8], right-hand side) elegantly demonstrates the conformational switch within the E1 that accompanies double-loading of the E1 with its cognate Ubl. The direction of the rearrangement of the UFD domain of UBA3 (that binds to the E2) as well as that in which the NEDD8 is passed on from the A site to the T site are indicated with arrows. The molecular surfaces of APPBP1 and UBA3 are highlighted in light cyan and grey, respectively. In the right-hand panel, the E2 Ubc12 is represented in turquoise. The UBA3 UFD domain (black) is shown in ribbon representation. Bound NEDD8 molecules are coloured red (A site) and orange (T site). (b) Comparison of singly charged E1 structures. Left panel: Uba1-Ub complex (PDB code 3CMM [10]). Right panel: APPBP1-UBA3-NEDD8-ATP complex. The bound small ubiquitin-like protein (Ub or NEDD8, respectively) is coloured red and the UFD domains of both E1 enzymes are coloured black. Within the E1 structures, the two juxtaposed catalytic cysteine half domains that compose the catalytic cysteine domain [19] are coloured pale yellow and light blue (respectively), the crossover loop that connects the adenylation and catalytic cysteine domains is coloured dark blue, and the molecular surface of the rest of the E1 is coloured grey (Uba1 and UBA3) and light cyan (APPBP1). A, adenylation; APPBP1, amyloid beta precursor protein-binding protein 1; NEDD8, neural precursor cell expressed, developmentally downregulated 8; PDB, Protein Data Bank; T, thioester; Ub, ubiquitin; Ubl, small ubiquitin-like protein; UBA3, ubiquitin-activating enzyme 3; UFD, ubiquitin-fold domain.

Mentions: The recent determination of the structure of a complex containing the NEDD8-E1 enzyme APPBP1-UBA3, a catalytically inactive variant of its cognate E2 (Ubc12), two NEDD8 molecules and Mg-ATP [8] (Figure 1a) elegantly demonstrated how a conformational change in an E1 can generate an affinity switch; only when the E1 is doubly loaded with its cognate Ubl does it acquire high affinity for its cognate E2. In this example, the APPBP1-UBA3 E1, once charged with two NEDD8 molecules at its adenylation (A)- and thioester (T)-active sites, transfers the (covalently bound) T-site NEDD8 to Ubc12 (an E2) and then adopts a conformation that promotes the release of the E2-Ubl conjugate. As the E2-binding sites for E1 and for E3 are mutually exclusive, the structure suggests that the E2 must dissociate from the E1 before it can associate with a cognate E3. Indeed, enzymological studies, at least in some cases, have shown that this is in fact the case [9].


All change: protein conformation and the ubiquitination reaction cascade.

Riedinger C, Endicott JA - F1000 Biol Rep (2009)

Conformational change accompanies catalysis in E1s(a) A conformational switch accompanies double-loading of an E1. A comparison of the structure of a singly loaded E1 complex (APPBP1-UBA3-NEDD8-ATP, PDB code 1R4N [11], left-hand side) and that of the doubly loaded complex (PDB code 2NVU [8], right-hand side) elegantly demonstrates the conformational switch within the E1 that accompanies double-loading of the E1 with its cognate Ubl. The direction of the rearrangement of the UFD domain of UBA3 (that binds to the E2) as well as that in which the NEDD8 is passed on from the A site to the T site are indicated with arrows. The molecular surfaces of APPBP1 and UBA3 are highlighted in light cyan and grey, respectively. In the right-hand panel, the E2 Ubc12 is represented in turquoise. The UBA3 UFD domain (black) is shown in ribbon representation. Bound NEDD8 molecules are coloured red (A site) and orange (T site). (b) Comparison of singly charged E1 structures. Left panel: Uba1-Ub complex (PDB code 3CMM [10]). Right panel: APPBP1-UBA3-NEDD8-ATP complex. The bound small ubiquitin-like protein (Ub or NEDD8, respectively) is coloured red and the UFD domains of both E1 enzymes are coloured black. Within the E1 structures, the two juxtaposed catalytic cysteine half domains that compose the catalytic cysteine domain [19] are coloured pale yellow and light blue (respectively), the crossover loop that connects the adenylation and catalytic cysteine domains is coloured dark blue, and the molecular surface of the rest of the E1 is coloured grey (Uba1 and UBA3) and light cyan (APPBP1). A, adenylation; APPBP1, amyloid beta precursor protein-binding protein 1; NEDD8, neural precursor cell expressed, developmentally downregulated 8; PDB, Protein Data Bank; T, thioester; Ub, ubiquitin; Ubl, small ubiquitin-like protein; UBA3, ubiquitin-activating enzyme 3; UFD, ubiquitin-fold domain.
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fig-001: Conformational change accompanies catalysis in E1s(a) A conformational switch accompanies double-loading of an E1. A comparison of the structure of a singly loaded E1 complex (APPBP1-UBA3-NEDD8-ATP, PDB code 1R4N [11], left-hand side) and that of the doubly loaded complex (PDB code 2NVU [8], right-hand side) elegantly demonstrates the conformational switch within the E1 that accompanies double-loading of the E1 with its cognate Ubl. The direction of the rearrangement of the UFD domain of UBA3 (that binds to the E2) as well as that in which the NEDD8 is passed on from the A site to the T site are indicated with arrows. The molecular surfaces of APPBP1 and UBA3 are highlighted in light cyan and grey, respectively. In the right-hand panel, the E2 Ubc12 is represented in turquoise. The UBA3 UFD domain (black) is shown in ribbon representation. Bound NEDD8 molecules are coloured red (A site) and orange (T site). (b) Comparison of singly charged E1 structures. Left panel: Uba1-Ub complex (PDB code 3CMM [10]). Right panel: APPBP1-UBA3-NEDD8-ATP complex. The bound small ubiquitin-like protein (Ub or NEDD8, respectively) is coloured red and the UFD domains of both E1 enzymes are coloured black. Within the E1 structures, the two juxtaposed catalytic cysteine half domains that compose the catalytic cysteine domain [19] are coloured pale yellow and light blue (respectively), the crossover loop that connects the adenylation and catalytic cysteine domains is coloured dark blue, and the molecular surface of the rest of the E1 is coloured grey (Uba1 and UBA3) and light cyan (APPBP1). A, adenylation; APPBP1, amyloid beta precursor protein-binding protein 1; NEDD8, neural precursor cell expressed, developmentally downregulated 8; PDB, Protein Data Bank; T, thioester; Ub, ubiquitin; Ubl, small ubiquitin-like protein; UBA3, ubiquitin-activating enzyme 3; UFD, ubiquitin-fold domain.
Mentions: The recent determination of the structure of a complex containing the NEDD8-E1 enzyme APPBP1-UBA3, a catalytically inactive variant of its cognate E2 (Ubc12), two NEDD8 molecules and Mg-ATP [8] (Figure 1a) elegantly demonstrated how a conformational change in an E1 can generate an affinity switch; only when the E1 is doubly loaded with its cognate Ubl does it acquire high affinity for its cognate E2. In this example, the APPBP1-UBA3 E1, once charged with two NEDD8 molecules at its adenylation (A)- and thioester (T)-active sites, transfers the (covalently bound) T-site NEDD8 to Ubc12 (an E2) and then adopts a conformation that promotes the release of the E2-Ubl conjugate. As the E2-binding sites for E1 and for E3 are mutually exclusive, the structure suggests that the E2 must dissociate from the E1 before it can associate with a cognate E3. Indeed, enzymological studies, at least in some cases, have shown that this is in fact the case [9].

Bottom Line: The structures of enzymes that collectively modify proteins by covalent addition of ubiquitin-like protein moieties have provided significant insights into the regulatory pathways they compose and have highlighted the importance of protein flexibility for the mechanism and regulation of the ubiquitination reaction.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Biophysics and Department of Biochemistry South Parks Road, Oxford OX1 3QU UK.

ABSTRACT
The structures of enzymes that collectively modify proteins by covalent addition of ubiquitin-like protein moieties have provided significant insights into the regulatory pathways they compose and have highlighted the importance of protein flexibility for the mechanism and regulation of the ubiquitination reaction.

No MeSH data available.


Related in: MedlinePlus