PDBsum entry 6itc

Protein transport

PDB id: 6itc

Contents

Protein chains

765 a.a.

420 a.a.

58 a.a.

116 a.a.

43 a.a.

225 a.a.

112 a.a.

Ligands

BEF

ADP

PGV ×2

Metals

_MG

PDB id:

6itc

Name:

Protein transport

Title:

Structure of a substrate engaged seca-secy protein translocation machine

Structure:

Protein translocase subunit seca. Chain: a. Engineered: yes. Protein translocase subunit secy. Chain: y. Engineered: yes. Mutation: yes. Protein translocase subunit sece. Chain: e.

Source:

Bacillus subtilis (strain 168). Organism_taxid: 224308. Strain: 168. Gene: seca, div+, bsu35300. Expressed in: escherichia coli #1/h766. Expression_system_taxid: 1354003. Geobacillus thermodenitrificans (strain ng80- 2). Organism_taxid: 420246.

Authors:

C.Y.Ma,X.F.Wu,D.J.Sun,E.Y.Park,T.A.Rapoport,N.Gao,L.Long

Key ref:

C.Ma et al. (2019). Structure of the substrate-engaged SecA-SecY protein translocation machine. Nat Commun, 10, 2872. PubMed id: 31253804 DOI: 10.1038/s41467-019-10918-2

Date:

21-Nov-18 Release date: 12-Jun-19

Protein chain

P28366  (SECA_BACSU) -  Protein translocase subunit SecA from Bacillus subtilis (strain 168)

Seq: 841 a.a.

Struc: 765 a.a.

Protein chain

A4IJK8  (A4IJK8_GEOTN) -  Protein translocase subunit SecY from Geobacillus thermodenitrificans (strain NG80-2)

Seq: 430 a.a.

Struc: 420 a.a.*

Protein chain

A4IJH4  (A4IJH4_GEOTN) -  Protein translocase subunit SecE from Geobacillus thermodenitrificans (strain NG80-2)

Seq: 60 a.a.

Struc: 58 a.a.

Protein chain

No UniProt id for this chain

Struc: 116 a.a.

Protein chain

P0A910  (OMPA_ECOLI) -  Outer membrane protein A from Escherichia coli (strain K12)

Seq: 346 a.a.

Struc: 43 a.a.*

Protein chain

P42212  (GFP_AEQVI) -  Green fluorescent protein from Aequorea victoria

Seq: 238 a.a.

Struc: 225 a.a.*

Protein chain

No UniProt id for this chain

Struc: 112 a.a.

* PDB and UniProt seqs differ at 31 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.7.4.2.8 - protein-secreting ATPase.
• Reaction: ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2

ATP + H2O + cellular proteinSide 1 = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + cellular proteinSide 2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41467-019-10918-2

Nat Commun 10:2872 (2019)

PubMed id: 31253804

Structure of the substrate-engaged SecA-SecY protein translocation machine.

C.Ma, X.Wu, D.Sun, E.Park, M.A.Catipovic, T.A.Rapoport, N.Gao, L.Li.

ABSTRACT

The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA's two-helix finger is close to the polypeptide, while SecA's clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel.