PDBsum entry 2e0x

Transferase

PDB id: 2e0x

Contents

Protein chains

359 a.a. *

178 a.a. *

Metals

_CA ×2

Waters ×432

* Residue conservation analysis

PDB id:

2e0x

Name:

Transferase

Title:

Crystal structure of gamma-glutamyltranspeptidase from escherichia coli (monoclinic form)

Structure:

Gamma-glutamyltranspeptidase. Chain: a, c. Fragment: large subunit. Engineered: yes. Gamma-glutamyltranspeptidase. Chain: b, d. Fragment: small subunit. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: ggt. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.95Å R-factor: 0.195 R-free: 0.231

Authors:

T.Okada,K.Wada,K.Fukuyama

Key ref:

T.Okada et al. (2007). Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism. J Biol Chem, 282, 2433-2439. PubMed id: 17135273 DOI: 10.1074/jbc.M607490200

Date:

16-Oct-06 Release date: 28-Nov-06

Protein chains

P18956  (GGT_ECOLI) -  Glutathione hydrolase proenzyme from Escherichia coli (strain K12)

Seq: 580 a.a.

Struc: 359 a.a.

Protein chains

P18956  (GGT_ECOLI) -  Glutathione hydrolase proenzyme from Escherichia coli (strain K12)

Seq: 580 a.a.

Struc: 178 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.2.3.2.2 - gamma-glutamyltransferase.
• Reaction: an N-terminal (5-L-glutamyl)-[peptide] + an alpha-amino acid = 5-L- glutamyl amino acid + an N-terminal L-alpha-aminoacyl-[peptide]
• Enzyme class 3: Chains A, B, C, D: E.C.3.4.19.13 - glutathione gamma-glutamate hydrolase.
• Reaction:
  1. glutathione + H2O = L-cysteinylglycine + L-glutamate
  2. an S-substituted glutathione + H2O = an S-substituted L-cysteinylglycine + L-glutamate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M607490200

J Biol Chem 282:2433-2439 (2007)

PubMed id: 17135273

Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism.

T.Okada, H.Suzuki, K.Wada, H.Kumagai, K.Fukuyama.

ABSTRACT

Gamma-glutamyltranspeptidase (GGT) is an extracellular enzyme that plays a key role in glutathione metabolism. The mature GGT is a heterodimer consisting of L- and S-subunits that is generated by posttranslational cleavage of the peptide bond between Gln-390 and Thr-391 in the precursor protein. Thr-391, which becomes the N-terminal residue of the S-subunit, acts as the active residue in the catalytic reaction. The crystal structure of a mutant GGT, T391A, that is unable to undergo autocatalytic processing, has been determined at 2.55-A resolution. Structural comparison of the precursor protein and mature GGT demonstrates that the structures of the core regions in the two proteins are unchanged, but marked differences are found near the active site. In particular, in the precursor, the segment corresponding to the C-terminal region of the L-subunit occupies the site where the loop (residues 438-449) forms the lid of the gamma-glutamyl group-binding pocket in the mature GGT. This result demonstrates that, upon cleavage of the N-terminal peptide bond of Thr-391, the newly produced C terminus (residues 375-390) flips out, allowing the 438-449 segment to form the gamma-glutamyl group-binding pocket. The electron density map for the T391A protein also identified a water molecule near the carbonyl carbon atom of Gln-390. The spatial arrangement around the water and Thr-391 relative to the scissile peptide bond appears suitable for the initiation of autocatalytic processing, as in other members of the N-terminal nucleophile hydrolase superfamily.

Selected figure(s)

Figure 1.
FIGURE 1. A stereo view of the F[o] – F[c] omit map around the processing site (A molecule). The map was generated on the basis of F[c] calculated from the model, which was derived from the refinement using REFMAC5 (23) omitting residues 385–392 and the water molecule (W4). The map was contoured at the 2.5 level. A ball-and-stick model of the T391A protein is overlaid on the map. The arrow indicates the scissile peptide bond that is cleaved in the wild-type precursor protein (Gln-390 to Thr-391). The figure was prepared using PYMOL (31).

Figure 2.
FIGURE 2. The tertiary structure of the T391A protein. A, a ribbon drawing of the T391A protein (B molecule). The segments in the T391A protein that correspond to the L- and S-subunits are pink and green, respectively, and the P-segment (residue 375–390) is highlighted in orange. Terminal residues that generate invisible segments are labeled. The orange arrow indicates the site at which autocatalytic processing occurs. B, a stereo view of the superimposition of C traces of the T391A protein and mature GGT. The structure of mature GGT (A molecule of SeMet-GGT in (19)) was superimposed on that of the T391A protein (B molecule). P-segment residues in the T391A protein and in mature GGT are orange and blue, respectively. Residues that had C atoms displaced by >1 Å upon processing are in yellow. Residues of mature GGT that are invisible in the T391A protein are shown in black. Regions of invisible residues are circled in green. The distance between Ser-387 C and Thr-391 N in mature GGT is shown. B is rotated by 30° around the vertical axis relative to A. C, a close-up view of the segment Glu-377 to Pro-380. A stick model of mature GGT (blue) is superimposed on the T391A protein (orange). The figures were prepared using PYMOL (31).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 2433-2439) copyright 2007.

Figures were selected by an automated process.