PDBsum entry 1v7x

Transferase

PDB id: 1v7x

Contents

Protein chain

779 a.a. *

Ligands

NDG

NAG

SO4

Metals

_CA ×2

Waters ×553

* Residue conservation analysis

PDB id:

1v7x

Name:

Transferase

Title:

Crystal structure of vibrio proteolyticus chitobiose phosphorylase in complex with glcnac and sulfate

Structure:

Chitobiose phosphorylase. Chain: a. Engineered: yes

Source:

Vibrio proteolyticus. Organism_taxid: 671. Gene: chbp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.163 R-free: 0.195

Authors:

M.Hidaka,Y.Honda,S.Nirasawa,M.Kitaoka,K.Hayashi,T.Wakagi,H.Shoun, S.Fushinobu

Key ref:

M.Hidaka et al. (2004). Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure, 12, 937-947. PubMed id: 15274915 DOI: 10.1016/j.str.2004.03.027

Date:

24-Dec-03 Release date: 22-Jun-04

Protein chain

Q76IQ9  (CHBP_VIBPR) -  N,N'-diacetylchitobiose phosphorylase from Vibrio proteolyticus

Seq: 801 a.a.

Struc: 779 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.280 - N,N'-diacetylchitobiose phosphorylase.
• Reaction: N,N'-diacetylchitobiose + phosphate = N-acetyl-alpha-D-glucosamine 1-phosphate + N-acetyl-D-glucosamine

N,N'-diacetylchitobiose + phosphate = N-acetyl-alpha-D-glucosamine 1-phosphate + N-acetyl-D-glucosamine (Bound ligand (Het Group name = NDG) corresponds exactly)

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

reference

DOI no: 10.1016/j.str.2004.03.027

Structure 12:937-947 (2004)

PubMed id: 15274915

Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.

M.Hidaka, Y.Honda, M.Kitaoka, S.Nirasawa, K.Hayashi, T.Wakagi, H.Shoun, S.Fushinobu.

ABSTRACT

Vibrio proteolyticus chitobiose phosphorylase (ChBP) belongs to glycosyl transferase family 36 (GT-36), and catalyzes the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. As the first known structures of a GT-36 enzyme, we determined the crystal structure of ChBP in a ternary complex with GlcNAc and SO(4). It is also the first structures of an inverting phosphorolytic enzyme in a complex with a sugar and a sulfate ion, and reveals a pseudo-ternary complex structure of enzyme-sugar-phosphate. ChBP comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain, constituting a distinctive structure among GT families. Instead, it shows significant structural similarity with glycoside hydrolase (GH) enzymes, glucoamylases (GH-15), and maltose phosphorylase (GH-65) in clan GH-L. The structural similarity reported here, together with distant sequence similarities between ChBP and GHs, led to the reclassification of family GT-36 into a novel GH family, namely GH-94.

Selected figure(s)

Figure 1.
Figure 1. Ribbon Diagrams of ChBP and Related Structures(A) Overall structure of the ChBP monomer (GlcNAc complex) shown as a ribbon model (N-terminal domain, blue; linker helices, green; a-helical barrel domain, yellow; C-terminal domain, red). The bound GlcNAc molecules (red), P394, and I417 (yellow) are shown as a ball-and-stick model, and the chloride (green) and calcium (black) ions are shown as a sphere. Residues between P394 and I417 are not included in the final model structure.(B) Ribbon diagram presentation of the ChBP dimer. The subunits are located around the crystallographic 2-fold axis. One subunit is colored as in (A), and the other one is colored white.(C) A ribbon diagram of bGA (1LF9; GH-15). Bacterial and archaeal glucoamylases comprise an N-terminal b sandwich domain (blue), linker helices (green), and an a-helical barrel domain (yellow), whereas fungal glucoamylases comprise only an a-helical barrel domain. The bound acarbose molecule (red) is shown as a ball-and-stick model.(D) A ribbon diagram of MalP (1H54; GH-65). The bound phosphate ion is shown as a ball-and-stick model. The domain constitution is identical with that of ChBP and each domain is colored as in (A).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 937-947) copyright 2004.

Figure was selected by the author.