PDBsum entry 3rui

Ligase

PDB id

3rui

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Contents

			Protein chains

					328 a.a.


					113 a.a.

			Metals

					_ZN

			Waters ×318

PDB id:

3rui

Links

Name:

Ligase

Title:

Crystal structure of atg7c-atg8 complex

Structure:

Ubiquitin-like modifier-activating enzyme atg7. Chain: a. Fragment: c-terminal domain (unp residues 293-630). Synonym: atg12-activating enzyme e1 atg7, autophagy-related protein 7, cytoplasm to vacuole targeting protein 2. Engineered: yes. Mutation: yes. Autophagy-related protein 8. Chain: b.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: s288c. Gene: atg7, apg7, cvt2, yhr171w. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: atg8, apg8, aut7, cvt5, ybl078c, ybl0732. Expression_system_taxid: 562

Resolution:

1.91Å

R-factor:

0.193

R-free:

0.218

Authors:

S.B.Hong,B.W.Kim,H.K.Song

Key ref:

S.B.Hong et al. (2011). Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8. Nat Struct Biol, 18, 1323-1330. PubMed id: 22056771

Date:

05-May-11

Release date:

23-Nov-11

PROCHECK

	Headers

	References

Protein chain

P38862 (ATG7_YEAST) - Ubiquitin-like modifier-activating enzyme ATG7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:

Seq: Struc:					630 a.a. 328 a.a.*

Protein chain

P38182 (ATG8_YEAST) - Autophagy-related protein 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					117 a.a. 113 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

	Nat Struct Biol 18:1323-1330 (2011)
PubMed id: 22056771

Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8.
S.B.Hong, B.W.Kim, K.E.Lee, S.W.Kim, H.Jeon, J.Kim, H.K.Song.

ABSTRACT

Autophagy is the degradation of cellular organelles via the lysosomal pathway. The autophagic ubiquitin-like (Ubl) molecule Atg8 is activated by the E1-like enzyme Atg7. As this noncanonical E1 enzyme's domain organization is unique among Ubl-activating E1 enzymes, the structural basis for its interactions with Atg8 and partner E2 enzymes remains obscure. Here we present the structure of the N-terminal domain of Atg7, revealing a unique protein fold and interactions with both autophagic E2 enzymes Atg3 and Atg10. The structure of the C-terminal domain of Atg7 in complex with Atg8 shows the mode of dimerization and mechanism of recognition of Atg8. Notably, the catalytic cysteine residue in Atg7 is positioned close to the C-terminal glycine of Atg8, its target for thioester formation, potentially eliminating the need for large conformational rearrangements characteristic of other E1s.

Literature references that cite this PDB file's key reference

PubMed id

Reference

23142983

M.Yamaguchi, K.Matoba, R.Sawada, Y.Fujioka, H.Nakatogawa, H.Yamamoto, Y.Kobashigawa, H.Hoshida, R.Akada, Y.Ohsumi, N.N.Noda, and F.Inagaki (2012).
Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.

Nat Struct Mol Biol, 19, 1250-1256.

23142976

S.E.Kaiser, K.Mao, A.M.Taherbhoy, S.Yu, J.L.Olszewski, D.M.Duda, I.Kurinov, A.Deng, T.D.Fenn, D.J.Klionsky, and B.A.Schulman (2012).
Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.

Nat Struct Mol Biol, 19, 1242-1249.

PDB codes:

4gsj 4gsk 4gsl

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.