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Structure paper

TitleConformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.
Journal, issue, pagesNat Struct Mol Biol, Vol. 27, Issue 5, Page 406-416, Year 2020
Publish dateApr 20, 2020
AuthorsKyle E Lopez / Alexandrea N Rizo / Eric Tse / JiaBei Lin / Nathaniel W Scull / Aye C Thwin / Aaron L Lucius / James Shorter / Daniel R Southworth /
PubMed AbstractThe ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ...The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop-substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis.
External linksNat Struct Mol Biol / PubMed:32313240 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.4 Å
Structure data

20845

6uqe

EMDB-20845, PDB-6uqe:
ClpA/ClpP Disengaged State bound to RepA-GFP
Method: EM (single particle) / Resolution: 3.0 Å

20851

6uqo

EMDB-20851, PDB-6uqo:
ClpA/ClpP Engaged State bound to RepA-GFP
Method: EM (single particle) / Resolution: 3.1 Å

21519

6w1z

EMDB-21519, PDB-6w1z:
ClpAP Engaged1 State bound to RepA-GFP
Method: EM (single particle) / Resolution: 2.7 Å

21520

6w20

EMDB-21520, PDB-6w20:
ClpAP Disengaged State bound to RepA-GFP
Method: EM (single particle) / Resolution: 3.0 Å

21521

6w21

EMDB-21521, PDB-6w21:
ClpAP Engaged2 State bound to RepA-GFP
Method: EM (single particle) / Resolution: 3.3 Å

21522

6w22

EMDB-21522, PDB-6w22:
ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)
Method: EM (single particle) / Resolution: 3.0 Å

21523

6w23

EMDB-21523, PDB-6w23:
ClpA Disengaged State bound to RepA-GFP (Focused Classification)
Method: EM (single particle) / Resolution: 3.1 Å

21524

6w24

EMDB-21524, PDB-6w24:
ClpA Engaged2 State bound to RepA-GFP (Focused Classification)
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Source
  • escherichia coli k-12 (bacteria)
  • unidentified (others)
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsCHAPERONE / AAA+ / Protease / Hsp100 / ATPase

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