PDBsum entry 3n2c

Hydrolase

PDB id: 3n2c

Contents

Protein chains

(+ 10 more) 408 a.a. *

Ligands

LWY ×16

Metals

_ZN ×32

* Residue conservation analysis

PDB id:

3n2c

Name:

Hydrolase

Title:

Crystal structure of prolidase eah89906 complexed with n- methylphosphonate-l-proline

Structure:

Prolidase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Engineered: yes

Source:

Unidentified. Organism_taxid: 32644. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.81Å R-factor: 0.222 R-free: 0.273

Authors:

Y.Patskovsky,C.Xu,J.M.Sauder,S.K.Burley,F.M.Raushel,S.C.Almo,New York Sgx Research Center For Structural Genomics (Nysgxrc)

Key ref:

D.F.Xiang et al. (2010). Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry, 49, 6791-6803. PubMed id: 20604542

Date:

17-May-10 Release date: 02-Jun-10

Supersedes:

3lwy

Protein chains

Q393A1  (Q393A1_BURL3) -  Amidohydrolase from Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)

Seq: 420 a.a.

Struc: 408 a.a.*

* PDB and UniProt seqs differ at 16 residue positions (black crosses)

Biochemistry 49:6791-6803 (2010)

PubMed id: 20604542

Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .

D.F.Xiang, Y.Patskovsky, C.Xu, A.A.Fedorov, E.V.Fedorov, A.A.Sisco, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel.

ABSTRACT

Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed and purified to homogeneity. The two proteins, Sgx9260c (gi|44242006) and Sgx9260b (gi|44479596), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of L-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-L-Pro, L-Ala-L-Pro and N-acyl derivatives of L-Pro. The best substrate identified to date is N-acetyl-L-Pro with a value of kcat/Km of 3 x 105 M-1 s-1. Sgx9260b catalyzes the hydrolysis of L-hydrophobic L-Pro dipeptides and N-acyl derivatives of L-Pro. The best substrate identified to date is N-propionyl-L-Pro with a value of kcat/Km of 1 x 105 M-1 s-1. Three dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes: 3MKV and 3FEQ). These proteins fold as distorted (beta/alpha)8-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methyl phosphonate derivative of L-Pro (PDB code: 3N2C). In this structure the phosphonate moiety bridges the binuclear metal center and one oxygen atom interacts with His-140. The alpha-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows beta-strand 7 within the (beta/alpha)8-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methyl phosphonate derivative of L-arginine (PDB code: 3MTW).