PDBsum entry 2d7r

Transferase

PDB id: 2d7r

Contents

Protein chain

536 a.a. *

Ligands

NAG-NAG

NAG ×2

NGA

UDP

SER-A2G

Metals

_MN

Waters ×74

* Residue conservation analysis

PDB id:

2d7r

Name:

Transferase

Title:

Crystal structure of pp-galnac-t10 complexed with galnac-ser on lectin domain

Structure:

Polypeptide n-acetylgalactosaminyltransferase 10. Chain: a. Fragment: residues 40-603. Synonym: protein-udp acetylgalactosaminyltransferase 10, udp- galnac:polypeptide n-acetylgalactosaminyltransferase 10, polypeptide galnac transferase 10, galnac-t10, pp-gantase 10. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

2.80Å R-factor: 0.229 R-free: 0.298

Authors:

T.Kubota,T.Shiba,S.Sugioka,R.Kato,S.Wakatsuki,H.Narimatsu

Key ref:

T.Kubota et al. (2006). Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10). J Mol Biol, 359, 708-727. PubMed id: 16650853 DOI: 10.1016/j.jmb.2006.03.061

Date:

25-Nov-05 Release date: 07-Nov-06

Protein chain

Q86SR1  (GLT10_HUMAN) -  Polypeptide N-acetylgalactosaminyltransferase 10 from Homo sapiens

Seq: 603 a.a.

Struc: 536 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.41 - polypeptide N-acetylgalactosaminyltransferase.
• Reaction:
  1. L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H⁺
  2. L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H⁺

L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H(+) (Bound ligand (Het Group name = UDP) corresponds exactly)

L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H(+) (Bound ligand (Het Group name = UDP) corresponds exactly)

• Cofactor: Ca(2+); Mn(2+)

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

Added reference

DOI no: 10.1016/j.jmb.2006.03.061

J Mol Biol 359:708-727 (2006)

PubMed id: 16650853

Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10).

T.Kubota, T.Shiba, S.Sugioka, S.Furukawa, H.Sawaki, R.Kato, S.Wakatsuki, H.Narimatsu.

ABSTRACT

Mucin-type O-glycans are important carbohydrate chains involved in differentiation and malignant transformation. Biosynthesis of the O-glycan is initiated by the transfer of N-acetylgalactosamine (GalNAc) which is catalyzed by UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-Ts). Here we present crystal structures of the pp-GalNAc-T10 isozyme, which has specificity for glycosylated peptides, in complex with the hydrolyzed donor substrate UDP-GalNAc and in complex with GalNAc-serine. A structural comparison with uncomplexed pp-GalNAc-T1 suggests that substantial conformational changes occur in two loops near the catalytic center upon donor substrate binding, and that a distinct interdomain arrangement between the catalytic and lectin domains forms a narrow cleft for acceptor substrates. The distance between the catalytic center and the carbohydrate-binding site on the lectin beta sub-domain influences the position of GalNAc glycosylation on GalNAc-glycosylated peptide substrates. A chimeric enzyme in which the two domains of pp-GalNAc-T10 are connected by a linker from pp-GalNAc-T1 acquires activity toward non-glycosylated acceptors, identifying a potential mechanism for generating the various acceptor specificities in different isozymes to produce a wide range of O-glycans.

Selected figure(s)

Figure 3.
Figure 3. Binding pocket for the donor substrate. UDP, GalNAc and Mn^2+ are shown in ball-and-stick representation in the same colors as for Figure 2. Amino acid residues interacting with the donor substrate are shown in a line representation (carbon atoms, green). Hydrogen-bonding interactions are shown as black broken lines. The coordinate bonds to Mn^2+ are represented as red broken lines. The oxygen atom of water molecule that coordinates the Mn^2+ is labeled with Wt. (a) and (b) Two views corresponding to those shown in Figure 2(a) and (b), respectively.

Figure 8.
Figure 8. Interactions between the catalytic domain, the linker region and the lectin domain. Ball-and-stick representations indicate residues responsible for the interactions, which are shown in red, blue and magenta for the catalytic domain, the linker region and the lectin domain, respectively. (a) pp-GalNAc-T10. Residues Asp289, Trp290, Lys295, Ile297, Pro298, Tyr404 and Arg408 are shown in red, Phe449TyrProProValGluProProAlaAlaAlaTrp460 in blue, and Thr504, Phe505, Trp507, Arg508, Ser540, Phe589, His591, Thr592, Asn593 and Val596 in magenta. (b) pp-GalNAc-T1. Residues Tyr256, Phe259, Trp261, Tyr268, Arg273, Met374, Phe377, Phe380, Ile383 and Glu416 are shown in red, Asp421SerGlnIleProArgHisTyrPheSerLeu431 in blue, and Gly464, Val467, Ser469, Tyr470, Thr471, Ala472, Arg477, Asp479, His499, Asn552 and Val553 in magenta.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 708-727) copyright 2006.

Figures were selected by an automated process.