PDBsum entry 2cb0

Isomerase

PDB id: 2cb0

Contents

Protein chains

320 a.a. *

Ligands

GOL

Waters ×290

* Residue conservation analysis

PDB id:

2cb0

Name:

Isomerase

Title:

Crystal structure of glucosamine 6-phosphate deaminase from pyrococcus furiosus

Structure:

Glucosamine-fructose-6-phosphate aminotransferase. Chain: a, b. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: dsm 3638

Resolution:

1.80Å R-factor: 0.172 R-free: 0.219

Authors:

K.J.Kim,M.H.Kim,B.S.Kang

Key ref:

K.J.Kim et al. (2007). The crystal structure of a novel glucosamine-6-phosphate deaminase from the hyperthermophilic archaeon Pyrococcus furiosus. Proteins, 68, 413-417. PubMed id: 17387737 DOI: 10.1002/prot.21322

Date:

23-Dec-05 Release date: 13-Mar-07

Protein chains

Q8U3U3  (Q8U3U3_PYRFU) -  Glucosamine-fructose-6-phosphate aminotransferase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 325 a.a.

Struc: 320 a.a.

DOI no: 10.1002/prot.21322

Proteins 68:413-417 (2007)

PubMed id: 17387737

The crystal structure of a novel glucosamine-6-phosphate deaminase from the hyperthermophilic archaeon Pyrococcus furiosus.

K.J.Kim, M.H.Kim, G.H.Kim, B.S.Kang.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Structures of glucosamine 6-phosphate deaminase from P. furiosus. (A) A polypeptide chain consisted of two similar five-stranded subdomains and C-terminal tail. N-terminal subdomain (red and yellow) and C-terminal subdomain (blue and magenta) were linked by short loop (gray) were followed by long C-terminal coil region (gray). (B) Twofold symmetrical interaction of two polypeptide chains (green and blue). A helix (yellow) from one chain interacts a cleft between N- and C-terminal subdomains of another chain (B_Nt and B_Ct) forming an active site (red circle). (C) A substrate, glucosamine 6-phosphate (yellow) from crystal structure of the isomerase of E. coli GlmS was superimposed on the active site of GlmD consisted of both monomers (green and blue). (D) C-terminal tail covers the substrate-binding site between two monomers (blue and green). Glucosamine 6-phosphate is placed to the binding pocket. Residue from other than a molecule containing sugar-binding site are indicated by asterisk. Residues D320, R324, and W325 from C-terminal region interact to K230, R226, and W249 from another monomer.

Figure 2.
Figure 2. The multiple sequence alignment of glucosamine 6-phsophate deaminases (GlmD) with glucosamine 6-phosphate synthases (GlmS). Amino acid sequences of the GlmD (1-325) from P. furiosus (Pfu_glmD), GlmD (1-326) and iosmerase domain (252-602) of GlmS from T. kodakaraensis (Tko_Glms and Tko_GlmD), and isomerase domain (249-608) of GlmS from E. coli (Eco_GlmS) were aligned. Numbering shown is from P. furiosus GlmD. Shown above alignments are elements of secondary structure of GlmD from P. furiosus. Residues involved in glucosamine 6-phsophate binding are marked with closed blue triangles. Multiple alignment was done using the T-coffe software and visualized using ESPript softwate both located on the ExPASy Proteomics Server (http://au.expasy.org/).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 413-417) copyright 2007.