PDBsum entry 1b54

Hypothetical protein

PDB id: 1b54

Contents

Protein chain

230 a.a. *

Ligands

PLP

Waters ×162

* Residue conservation analysis

PDB id:

1b54

Name:

Hypothetical protein

Title:

Crystal structure of a yeast hypothetical protein-a structure from bnl's human proteome project

Structure:

Yeast hypothetical protein. Chain: a. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c. Gene: sgd: ybl 036c. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: chr ii gene obtained by pcr from s288c genomic DNA cloned into t7 expression vector pet13a at ndei-bamhi sites, no

Resolution:

2.10Å R-factor: 0.235 R-free: 0.303

Authors:

S.Swaminathan,S.Eswaramoorthy,S.K.Burley,New York Sgx Research Center For Structural Genomics (Nysgxrc)

Key ref:

S.Eswaramoorthy et al. (2003). Structure of a yeast hypothetical protein selected by a structural genomics approach. Acta Crystallogr D Biol Crystallogr, 59, 127-135. PubMed id: 12499548 DOI: 10.1107/S0907444902018012

Date:

12-Jan-99 Release date: 27-Jan-99

Protein chain

P38197  (PLPHP_YEAST) -  Pyridoxal phosphate homeostasis protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 257 a.a.

Struc: 230 a.a.

DOI no: 10.1107/S0907444902018012

Acta Crystallogr D Biol Crystallogr 59:127-135 (2003)

PubMed id: 12499548

Structure of a yeast hypothetical protein selected by a structural genomics approach.

S.Eswaramoorthy, S.Gerchman, V.Graziano, H.Kycia, F.W.Studier, S.Swaminathan.

ABSTRACT

Yeast hypothetical protein YBL036C (SWISS-PROT P38197), initially thought to be a member of an 11-protein family, was selected for crystal structure determination since no structural or functional information was available. The structure has been determined independently by MIR and MAD methods to 2.0 A resolution. The MAD structure was determined largely through automated model building. The protein folds as a TIM barrel beginning with a long N-terminal helix, in contrast to the classic triose phosphate isomerase (TIM) structure, which begins with a beta-strand. A cofactor, pyridoxal 5'-phosphate, is covalently bound near the C-terminal end of the barrel, the usual active site in TIM-barrel folds. A single-domain monomeric molecule, this yeast protein resembles the N-terminal domain of alanine racemase or ornithine decarboxylase, both of which are two-domain dimeric proteins. The yeast protein has been shown to have amino-acid racemase activity. Although selected as a member of a protein family having no obvious relationship to proteins of known structure, the protein fold turned out to be a well known and widely distributed fold. This points to the need for a more comprehensive base of structural information and better structure-modeling tools before the goal of structure prediction from amino-acid sequences can be realised. In this case, similarity to a known structure allowed inferences to be made about the structure and function of a widely distributed protein family.

Selected figure(s)

Figure 3.
Figure 3 (a) A schematic diagram with the numbering scheme of PLP. (b) Stereoview of the active site of the yeast protein P007. The cofactor and residues involved in the active site are shown as a ball-and-stick model along with the C^ trace of the protein. The cofactor PLP is covalently bound to Lys49 and makes a hydrogen bond with Arg239. The phosphate group interacts with Ser224 and Thr242. The O3 of the pyridine ring makes a hydrogen bond to Asp70.

Figure 4.
Figure 4 Superposition of P007 and the TIM-barrel domain of ARC shows similarity near the active site. The helices and the strands at the other side deviate considerably. The brute-force alignment of LSQMAN matched 154 atoms with an r.m.s.d. of 1.72 Å.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 127-135) copyright 2003.

Figures were selected by an automated process.