PDBsum entry 1k77

Structural genomics, unknown function

PDB id: 1k77

Contents

Protein chain

260 a.a. *

Ligands

GOL ×2

FMT

Metals

_MG ×2

Waters ×272

* Residue conservation analysis

PDB id:

1k77

Name:

Structural genomics, unknown function

Title:

Crystal structure of ec1530, a putative oxygenase from escherichia coli

Structure:

Hypothetical protein ygbm. Chain: a. Synonym: ec1530. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.63Å R-factor: 0.194 R-free: 0.214

Authors:

Y.Kim,T.Skarina,S.Beasley,R.Laskowski,C.H.Arrowsmith,A.Joachimiak, A.M.Edwards,A.Savchenko,Midwest Center For Structural Genomics (Mcsg)

Key ref:

Y.Kim et al. (2002). Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM. Proteins, 48, 427-430. PubMed id: 12112708 DOI: 10.1002/prot.10160

Date:

18-Oct-01 Release date: 13-Mar-02

Protein chain

Q46891  (OTNI_ECOLI) -  2-oxo-tetronate isomerase from Escherichia coli (strain K12)

Seq: 258 a.a.

Struc: 260 a.a.

Enzyme reactions

• Enzyme class: E.C.5.3.1.35 - 2-dehydrotetronate isomerase.
• Reaction:
  1. 2-dehydro-L-erythronate = 3-dehydro-L-erythronate
  2. 2-dehydro-D-erythronate = 3-dehydro-D-erythronate

DOI no: 10.1002/prot.10160

Proteins 48:427-430 (2002)

PubMed id: 12112708

Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.

Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Joachimiak, A.Edwards, A.Savchenko.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. A: Protein sequences are compared between different species. B: The ribbon drawing shows the TIM structure of EC1530. -helices, outside of the barrel, are shown in red, -strands, inside of the barrel in cyan, and one of two Mg^2+ (the major site) in the barrel is shown in green. The Mg^2+ in the minor site located on the outside surface is not shown. C: The secondary elements were indicated above the one-letter amino acid codes of E. coli ygbM. Residues interacting with Mg^2+ are also indicated in red dots.

Figure 2.
Figure 2. Putative catalytic site including Mg^2+ (major site) is shown. The Mg^2+ is coordinated to an ordered water molecule, a formate, two glutamate, a glutamine, aspartate residues forming a square-bi-pyramid conformation.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2002, 48, 427-430) copyright 2002.