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PDBsum entry 4b0t
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PDB id:
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Ligase
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Title:
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Structure of the pup ligase pafa of the prokaryotic ubiquitin-like modification pathway in complex with adp
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Structure:
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Pup--protein ligase. Chain: a, b. Synonym: pafa, proteasome accessory factor a, pup-conjugating enzyme. Engineered: yes
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Source:
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Corynebacterium glutamicum. Organism_taxid: 1718. Atcc: 13032. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta.
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Resolution:
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2.16Å
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R-factor:
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0.179
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R-free:
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0.219
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Authors:
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D.Ozcelik,J.Barandun,N.Schmitz,M.Sutter,E.Guth,F.F.Damberger,F.H.- T.Allain,N.Ban,E.Weber-Ban
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Key ref:
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D.Özcelik
et al.
(2012).
Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway.
Nat Commun,
3,
1014.
PubMed id:
DOI:
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Date:
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04-Jul-12
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Release date:
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12-Sep-12
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PROCHECK
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Headers
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References
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Q8NQE1
(PAFA_CORGL) -
Pup--protein ligase from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)
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Seq:
Struc:
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482 a.a.
470 a.a.
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Enzyme class:
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E.C.6.3.1.19
- prokaryotic ubiquitin-like protein ligase.
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Reaction:
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L- lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]- gamma-L-glutamyl)-[protein]-L-lysine
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ATP
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+
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[prokaryotic ubiquitin-like protein]-L-glutamate
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+
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[protein]-L- lysine
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=
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ADP
Bound ligand (Het Group name = )
corresponds exactly
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phosphate
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+
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N(6)-([prokaryotic ubiquitin-like protein]- gamma-L-glutamyl)-[protein]-L-lysine
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Nat Commun
3:1014
(2012)
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PubMed id:
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Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway.
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D.Özcelik,
J.Barandun,
N.Schmitz,
M.Sutter,
E.Guth,
F.F.Damberger,
F.H.Allain,
N.Ban,
E.Weber-Ban.
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ABSTRACT
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Pupylation is a posttranslational protein modification occurring in mycobacteria
and other actinobacteria that is functionally analogous to ubiquitination. Here
we report the crystal structures of the modification enzymes involved in this
pathway, the prokaryotic ubiquitin-like protein (Pup) ligase PafA and the
depupylase/deamidase Dop. Both feature a larger amino-terminal domain consisting
of a central β-sheet packed against a cluster of helices, a fold characteristic
for carboxylate-amine ligases, and a smaller C-terminal domain unique to
PafA/Dop members. The active site is located on the concave surface of the
β-sheet with the nucleotide bound in a deep pocket. A conserved groove leading
into the active site could have a role in Pup-binding. Nuclear magnetic
resonance and biochemical experiments determine the region of Pup that interacts
with PafA and Dop. Structural data and mutational studies identify crucial
residues for the catalysis of both enzymes.
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