PDBsum entry 1nkt

Protein transport

PDB id: 1nkt

Contents

Protein chains

836 a.a. *

Ligands

ADP ×2

Metals

_MG ×2

Waters ×546

* Residue conservation analysis

PDB id:

1nkt

Name:

Protein transport

Title:

Crystal structure of the seca protein translocation atpase from mycobacterium tuberculosis complex with adpbs

Structure:

Preprotein translocase seca 1 subunit. Chain: a, b. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: seca1 or seca or rv3240c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.216 R-free: 0.265

Authors:

V.Sharma,A.Arockiasamy,D.R.Ronning,C.G.Savva,A.Holzenburg, M.Braunstein,W.R.Jacobs Jr.,J.C.Sacchettini,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

V.Sharma et al. (2003). Crystal structure of Mycobacterium tuberculosis SecA, a preprotein translocating ATPase. Proc Natl Acad Sci U S A, 100, 2243-2248. PubMed id: 12606717 DOI: 10.1073/pnas.0538077100

Date:

03-Jan-03 Release date: 04-Mar-03

Protein chains

P9WGP5  (SECA1_MYCTU) -  Protein translocase subunit SecA 1 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 949 a.a.

Struc: 836 a.a.*

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

Enzyme reactions

• Enzyme class: 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: 10.1073/pnas.0538077100

Proc Natl Acad Sci U S A 100:2243-2248 (2003)

PubMed id: 12606717

Crystal structure of Mycobacterium tuberculosis SecA, a preprotein translocating ATPase.

V.Sharma, A.Arockiasamy, D.R.Ronning, C.G.Savva, A.Holzenburg, M.Braunstein, W.R.Jacobs, J.C.Sacchettini.

ABSTRACT

In bacteria, the majority of exported proteins are translocated by the Sec system, which recognizes the signal sequence of a preprotein and uses ATP and the proton motive force to mediate protein translocation across the cytoplasmic membrane. SecA is an essential protein component of this system, containing the molecular motor that facilitates translocation. Here we report the three-dimensional structure of the SecA protein of Mycobacterium tuberculosis. Each subunit of the homodimer contains a "motor" domain and a translocation domain. The structure predicts that SecA can interact with the SecYEG pore and function as a molecular ratchet that uses ATP hydrolysis for physical movement of the preprotein. Knowledge of this structure provides a framework for further elucidation of the translocation process.

Selected figure(s)

Figure 4.
Fig. 4. Comparison of the binding site of tbSecA:ADP- -S (a) with PcrA:ATP (b). (a) Stereo diagram of a stick representation of the binding site of tbSecA:ADP- -S shows the residues involved in the ADP binding. Most of the contacts from NBD1 are from Walker A (cyan), Walker B (purple), and adenine binding (green) loops. (b) Similar representation of binding of ATP analog ADPNP to PcrA helicase (42). The side chains that make contact with the -phosphate are Q254, R287, and R610 and have counterparts in SecA (Q566, R490, and R570).

Figure 5.
Fig. 5. A mechanical drawing depicting our model of the motor movements associated with the ADP and ATP bound states of SecA. (a) The red tubes represent the regions of the connecting structure of SecA observed in the ADP bound state. (b) In transparent violet are the corresponding regions of our model of the protein with ATP bound. The movements of the motor domain as described in the text are transmitted to the translation domain via the long 25-helix and the two connecting -strands shown atop the silver pipe, which is the conserved pore found in the SSD. In dark blue is the pivot arm groove from the adjacent subunit of the dimer.

Figures were selected by an automated process.