PDBsum entry 1qq9

Hydrolase

PDB id: 1qq9

Contents

Protein chain

277 a.a. *

Ligands

MET

Metals

_ZN ×2

_CA

Waters ×291

* Residue conservation analysis

PDB id:

1qq9

Name:

Hydrolase

Title:

Streptomyces griseus aminopeptidase complexed with methionine

Structure:

Aminopeptidase. Chain: a. Synonym: sgap. Ec: 3.4.11.-

Source:

Streptomyces griseus. Organism_taxid: 1911. Other_details: the enzyme is isolated from the commercially available enzyme mixture "pronase e"

Resolution:

1.53Å R-factor: 0.148 R-free: 0.173

Authors:

R.Gilboa,H.M.Greenblatt,M.Perach,A.Spungin-Bialik,U.Lessel, D.Schomburg,S.Blumberg,G.Shoham

Key ref:

R.Gilboa et al. (2000). Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 A resolution. Acta Crystallogr D Biol Crystallogr, 56, 551-558. PubMed id: 10771423 DOI: 10.1107/S0907444900002420

Date:

12-Jun-99 Release date: 03-May-00

Protein chain

P80561  (APX_STRGG) -  Aminopeptidase S from Streptomyces griseus subsp. griseus (strain JCM 4626 / CBS 651.72 / NBRC 13350 / KCC S-0626 / ISP 5235)

Seq: 445 a.a.

Struc: 277 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.11.24 - aminopeptidase S.
• Cofactor: Zn(2+)

DOI no: 10.1107/S0907444900002420

Acta Crystallogr D Biol Crystallogr 56:551-558 (2000)

PubMed id: 10771423

Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 A resolution.

R.Gilboa, H.M.Greenblatt, M.Perach, A.Spungin-Bialik, U.Lessel, G.Wohlfahrt, D.Schomburg, S.Blumberg, G.Shoham.

ABSTRACT

SGAP is an aminopeptidase present in the extracellular fluid of Streptomyces griseus cultures. It is a double-zinc enzyme with a strong preference for large hydrophobic amino-terminus residues. It is a monomeric (30 kDa) heat-stable enzyme, with a high and efficient catalytic activity modulated by calcium ions. The small size, high activity and heat stability make SGAP a very attractive enzyme for various biotechnological applications. Only one other related aminopeptidase (Aeromonas proteolytica AP; AAP) has been structurally analyzed to date and its structure was shown to be considerably similar to SGAP, despite the low sequence homology between the two enzymes. The motivation for the detailed structural analysis of SGAP originated from a strong mechanistic interest in the family of double-zinc aminopeptidases, combined with the high potential applicability of these enzymes. The 1.75 A crystallographic structure of native SGAP has been previously reported, but did not allow critical mechanistic interpretations owing to inconclusive structural regions around the active site. A more accurate structure of SGAP at 1.58 A resolution is reported in this paper, along with the 1.53 A resolution structure of the SGAP complex with inhibitory methionine, which is also a product of the SGAP catalytic process. These two high-resolution structures enable a better understanding of the SGAP binding mode of both substrates and products. These studies allowed the tracing of the previously disordered region of the enzyme (Glu196-Arg202) and the identification of some of the functional groups of the enzyme that are involved in enzyme-substrate interactions (Asp160, Met161, Gly201, Arg202 and Phe219). These studies also suggest that Glu131 is directly involved in the catalytic mechanism of SGAP, probably as the hydrolytic nucleophile. The structural results are compared with a recent structure of AAP with an hydroxamate inhibitor in order to draw general functional conclusions which are relevant for this family of low molecular-weight aminopeptidases.

Selected figure(s)

Figure 3.
Figure 3 Stereoview of the SGAP active site. The refined new structure of the native enzyme at 1.58 Å (blue) is superimposed on the old structure of the native enzyme at 1.75 Å (green). It is demonstrated that most of the active site is identical, except for the non-protein ligand of the active-site zinc ions [a phosphate ion (PO4) for the old structure and a water molecule (WAT) for the new structure] observed approximately in the same coordination site between the two metal ions (Zn1 and Zn2). The difference in this zinc ligand is probably the main factor causing positional differences for the active-site water molecules between the old (green) and the new (blue) structures.

Figure 6.
Figure 6 Interactions of the bound methionine with SGAP as demonstrated in a schematic diagram of the active-site region of the SGAP-Met complex. The protein bonds are shown in blue, the bound methionine (Met) bonds are shown in orange, the Zn atoms are shown in purple, while the rest of the atoms are in the standard atomic colors. Dashed lines indicate hydrogen bonds or ionic interactions, while `radiating' spheres indicate hydrophobic contacts between the bound methionine (small spheres) and the neighbouring protein groups (larger spheres). [This figure was prepared with the program Ligplot (Wallace et al., 1995[Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.]).]

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 551-558) copyright 2000.

Figures were selected by an automated process.