PDBsum entry 1ofi

Hydrolase

PDB id: 1ofi

Contents

Protein chains

299 a.a. *

(+ 0 more) 174 a.a. *

Ligands

ADP ×3

PO4 ×3

LVS ×3

Metals

_MG ×12

Waters ×21

* Residue conservation analysis

PDB id:

1ofi

Name:

Hydrolase

Title:

Asymmetric complex between hslv and i-domain deleted hslu (h. Influenzae)

Structure:

Atp-dependent hsl protease atp-binding subunit hslu. Chain: a, b, c. Engineered: yes. Atp-dependent protease hslv. Chain: g, h, i, l, m, n. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 71421. Strain: rd. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

80mer (from PDB file)

Resolution:

3.20Å R-factor: 0.232 R-free: 0.327

Authors:

A.R.Kwon,B.M.Kessler,H.S.Overkleeft,D.B.Mckay

Key ref:

A.R.Kwon et al. (2003). Structure and reactivity of an asymmetric complex between HslV and I-domain deleted HslU, a prokaryotic homolog of the eukaryotic proteasome. J Mol Biol, 330, 185-195. PubMed id: 12823960 DOI: 10.1016/S0022-2836(03)00580-1

Date:

14-Apr-03 Release date: 03-Jul-03

Protein chains

P43773  (HSLU_HAEIN) -  ATP-dependent protease ATPase subunit HslU from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 444 a.a.

Struc: 299 a.a.*

Protein chains

P43772  (HSLV_HAEIN) -  ATP-dependent protease subunit HslV from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 175 a.a.

Struc: 174 a.a.

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

Enzyme reactions

• Enzyme class: Chains G, H, I, L, M, N: E.C.3.4.25.2 - HslU--HslV peptidase.

DOI no: 10.1016/S0022-2836(03)00580-1

J Mol Biol 330:185-195 (2003)

PubMed id: 12823960

Structure and reactivity of an asymmetric complex between HslV and I-domain deleted HslU, a prokaryotic homolog of the eukaryotic proteasome.

A.R.Kwon, B.M.Kessler, H.S.Overkleeft, D.B.McKay.

ABSTRACT

In the prokaryotic homolog of the eukaryotic proteasome, HslUV, the "double donut" HslV protease is allosterically activated by HslU, an AAA protein of the Clp/Hsp100 family consisting of three (amino-terminal, carboxy-terminal, and intermediate) domains. The intermediate domains of HslU, which extend like tentacles from the hexameric ring formed by the amino-terminal and carboxy-terminal domains, have been deleted; an asymmetric HslU(DeltaI)(6)HslV(12) complex has been crystallized; and the structure has been solved to 2.5A resolution, revealing an assembly in which a HslU(DeltaI) hexamer binds one end of the HslV dodecamer. The conformation of the protomers of the HslU(DeltaI)-complexed HslV hexamer is similar to that in the symmetric wild-type HslUV complex, while the protomer conformation of the uncomplexed HslV hexamer is similar to that of HslV alone. Reaction in the crystals with a vinyl sulfone inhibitor reveals that the HslU(DeltaI)-complexed HslV hexamer is active, while the uncomplexed HslV hexamer is inactive. These results confirm that HslV can be activated by binding of a hexameric HslU(DeltaI)(6) ring lacking the I domains, that activation is effected through a conformational change in HslV rather than through alteration of the size of the entry channel into the protease catalytic cavity, and that the two HslV(6) rings in the protease dodecamer are activated independently rather than cooperatively.

Selected figure(s)

Figure 2.
Figure 2. Structure of the HslU(DI)[6]HslV[12] complex. (a) A drawing of one complex viewed perpendicular to the 6-fold axis, with a-helices represented as cylinders. Color scheme: HslU(DI), magenta with one subunit blue; HslU(DI)-complexed HslV, yellow with one subunit red; uncomplexed HslV, cyan with one subunit green. (b) View of one HslU(DI)[6] hexamer looking parallel with the 6-fold axis. (c) HslU(DI)-complexed HslV hexamer viewed from the top of the molecules. (d) Uncomplexed HslV hexamer viewed from the bottom of the molecule.

Figure 4.
Figure 4. NLVS inhibitor. (a) F[o] -F[c] electron density map contoured at 2.6s, computed using calculated phases from model without inhibitor, showing that inhibitor is present in upper hexamer only. The two pairs of crystallographically independent HslV subunits of the HslU(DI)[6]HslV[12] complex that is aligned along the 3-fold axis are shown; subunits from HslU(DI)-complexed HslV are red and yellow; from uncomplexed HslV, green and cyan. Thr1, with which the inhibitor reacts, shown in magenta in all subunits. (b) Ribbon drawing of superposition of HslU(DI)-complexed and uncomplexed HslV, with NLVS inhibitor. Where HslV protomers are similar in conformation, as originally defined by Sousa et al.,[15.] structure is green; where they differ, HslU(DI)-complexed HslV is blue; uncomplexed HslV is yellow. Inhibitor model is red. (c) Stereo view of superposition of complexed and uncomplexed HslV near inhibitor. Selected amino acid side-chains and segments of polypeptide backbone that hydrogen-bond the inhibitor are shown. For a detailed description of interactions with inhibitor, see Sousa et al.[23.] C^a backbone trace of HslU(DI)-complexed subunits, cyan; backbone trace of uncomplexed subunits, yellow; carbon atoms of inhibitor, magenta; carbon atoms of amino acid side-chains, green; oxygen atoms, red; nitrogen atoms, blue; sulfur atoms, yellow; iodine atoms, purple.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 185-195) copyright 2003.

Figures were selected by an automated process.