PDBsum entry 5ayc

Transferase

PDB id: 5ayc

Contents

Protein chain

386 a.a.

Ligands

BGC-BMA

SO4

Waters ×458

PDB id:

5ayc

Name:

Transferase

Title:

Crystal structure of ruminococcus albus 4-o-beta-d-mannosyl-d-glucose phosphorylase (ramp1) in complexes with sulfate and 4-o-beta-d- mannosyl-d-glucose

Structure:

4-o-beta-d-mannosyl-d-glucose phosphorylase. Chain: a. Synonym: mannosylglucose phosphorylase,ramp1. Engineered: yes

Source:

Ruminococcus albus (strain atcc 27210 / dsm 20455 / jcm 14654 / ncdo 2250 / 7). Organism_taxid: 697329. Strain: atcc 27210 / dsm 20455 / jcm 14654 / ncdo 2250 / 7. Gene: rumal_0852. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.155 R-free: 0.197

Authors:

Y.Ye,W.Saburi,K.Kato,M.Yao

Key ref:

Y.Ye et al. (2016). Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies. Febs Lett, 590, 828-837. PubMed id: 26913570 DOI: 10.1002/1873-3468.12105

Date:

13-Aug-15 Release date: 23-Mar-16

Protein chain

E6UIS7  (MGP_RUMA7) -  4-O-beta-D-mannosyl-D-glucose phosphorylase from Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7)

Seq: 386 a.a.

Struc: 386 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.281 - 4-O-beta-D-mannosyl-D-glucose phosphorylase.
• Reaction: 4-O-beta-D-mannopyranosyl-D-glucopyranose + phosphate = alpha-D-mannose 1-phosphate + D-glucose

4-O-beta-D-mannopyranosyl-D-glucopyranose + phosphate = alpha-D-mannose 1-phosphate + D-glucose (Bound ligand (Het Group name = BGC) corresponds exactly)

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

reference

DOI no: 10.1002/1873-3468.12105

Febs Lett 590:828-837 (2016)

PubMed id: 26913570

Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.

Y.Ye, W.Saburi, R.Odaka, K.Kato, N.Sakurai, K.Komoda, M.Nishimoto, M.Kitaoka, H.Mori, M.Yao.

ABSTRACT

In Ruminococcus albus, 4-O-β-d-mannosyl-d-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-d-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.