PDBsum entry 4mnc

Transport protein

PDB id: 4mnc

Contents

Protein chain

305 a.a.

Ligands

173 ×2

SO4 ×3

Waters ×556

PDB id:

4mnc

Name:

Transport protein

Title:

Crystal structure of a trap periplasmic solute binding protein from polaromonas sp. Js666 (bpro_4736), target efi-510156, with bound benzoyl formate, space group p21

Structure:

Trap dicarboxylate transporter-dctp subunit. Chain: a. Synonym: trap periplasmic solute binding protein. Engineered: yes

Source:

Polaromonas sp.. Organism_taxid: 296591. Strain: js666 / atcc baa-500. Gene: bpro_4736. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.05Å R-factor: 0.129 R-free: 0.144

Authors:

M.W.Vetting,R.Toro,R.Bhosle,N.F.Al Obaidi,L.L.Morisco,S.R.Wasserman, S.Sojitra,S.Zhao,M.Stead,A.Scott Glenn,S.Chowdhury,B.Evans, B.Hillerich,J.Love,R.D.Seidel,H.J.Imker,M.P.Jacobson,J.A.Gerlt, S.C.Almo,Enzyme Function Initiative (Efi)

Key ref:

M.W.Vetting et al. (2015). Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry, 54, 909-931. PubMed id: 25540822 DOI: 10.1021/bi501388y

Date:

10-Sep-13 Release date: 25-Sep-13

Protein chain

Q122C7  (DCTP2_POLSJ) -  Solute-binding protein Bpro_4736 from Polaromonas sp. (strain JS666 / ATCC BAA-500)

Seq: 325 a.a.

Struc: 305 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/bi501388y

Biochemistry 54:909-931 (2015)

PubMed id: 25540822

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

M.W.Vetting, N.Al-Obaidi, S.Zhao, B.San Francisco, J.Kim, D.J.Wichelecki, J.T.Bouvier, J.O.Solbiati, H.Vu, X.Zhang, D.A.Rodionov, J.D.Love, B.S.Hillerich, R.D.Seidel, R.J.Quinn, A.L.Osterman, J.E.Cronan, M.P.Jacobson, J.A.Gerlt, S.C.Almo.

ABSTRACT

The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.