PDBsum entry 1vkh

Hydrolase

PDB id: 1vkh

Contents

Protein chains

261 a.a. *

Ligands

GOL ×2

Metals

_CL

Waters ×458

* Residue conservation analysis

PDB id:

1vkh

Name:

Hydrolase

Title:

Crystal structure of a putative serine hydrolase (ydr428c) from saccharomyces cerevisiae at 1.85 a resolution

Structure:

Putative serine hydrolase. Chain: a, b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ydr428c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.85Å R-factor: 0.145 R-free: 0.189

Authors:

Joint Center For Structural Genomics (Jcsg)

Key ref:

J.W.Arndt et al. (2005). Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution. Proteins, 58, 755-758. PubMed id: 15624212 DOI: 10.1002/prot.20336

Date:

20-May-04 Release date: 08-Jun-04

Protein chains

Q04066  (KFA_YEAST) -  Kynurenine formamidase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 261 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.1.9 - arylformamidase.
• Pathway: Tryptophan Catabolism
• Reaction: N-formyl-L-kynurenine + H2O = L-kynurenine + formate + H⁺

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

reference

DOI no: 10.1002/prot.20336

Proteins 58:755-758 (2005)

PubMed id: 15624212

Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.

J.W.Arndt, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, L.Jaroszewski, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, W.S.Peti, K.Quijano, R.Reyes, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of YDR428C. A: Stereoview of ribbon diagram of Saccharomyces cerevisiae YDR428C color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. -Helices H1-H12, and -strands ( 1- 7) are indicated. B: Diagram showing the secondary structure elements in YDR428C superimposed on its primary sequence. The -helices, 3[10]-helices, -sheet strands (red A), -bulges, and -turns are indicated. The disordered regions are depicted by a dashed line with the corresponding sequence in brackets.

Figure 2.
Figure 2. A: Ribbon diagram of a superposition of YDR428C (blue) and P. fluorescens carboxylesterase (grey). Residues of the catalytic triad, shown in ball and stick, indicate the active site location. B: Same as A, but a close up view of the catalytic triad. Active site residues as observed in P. fluorescens carboxylesterase (PDB 1auo; grey; P. fluorescens residues shown in parenthesis) and their counterparts in YDR428C (blue) are shown in ball and stick. Hydrogen bond interactions and distances are indicated. C: Ribbon diagram of the YDR428C dimer. 7 strands and helices H10 and H12 forming part of the dimer interface and locations of active sites (arrow) are indicated.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 755-758) copyright 2005.