PDBsum entry 2ffv

Transferase

PDB id: 2ffv

Contents

Protein chain

489 a.a. *

Ligands

UDP ×2

Metals

_MN ×2

* Residue conservation analysis

PDB id:

2ffv

Name:

Transferase

Title:

Human ppgalnact-2 complexed with manganese and udp

Structure:

Polypeptide n-acetylgalactosaminyltransferase 2. Chain: a, b. Fragment: catalytic and lectin domains. Synonym: ppgalnact-2. Protein-udp acetylgalactosaminyltransferase 2. Udp-galnac:polypeptide n-acetylgalactosaminyltransferase 2. Polypeptide galnac transferase 2. Galnac-t2. Pp-gantase 2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: galnt2. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Other_details: invitrogen ppic9 vector with tev-protease-cleavable, n-terminal engineered 6his tag

Biol. unit:

Tetramer (from PQS)

Resolution:

2.75Å R-factor: 0.225 R-free: 0.286

Authors:

T.A.Fritz

Key ref:

T.A.Fritz et al. (2006). Dynamic association between the catalytic and lectin domains of human UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase-2. J Biol Chem, 281, 8613-8619. PubMed id: 16434399 DOI: 10.1074/jbc.M513590200

Date:

20-Dec-05 Release date: 31-Jan-06

Protein chains

Q10471  (GALT2_HUMAN) -  Polypeptide N-acetylgalactosaminyltransferase 2 from Homo sapiens

Seq: 571 a.a.

Struc: 489 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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: 10.1074/jbc.M513590200

J Biol Chem 281:8613-8619 (2006)

PubMed id: 16434399

Dynamic association between the catalytic and lectin domains of human UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase-2.

T.A.Fritz, J.Raman, L.A.Tabak.

ABSTRACT

The family of UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (ppGalNAcTs) is unique among glycosyltransferases, containing both catalytic and lectin domains that we have previously shown to be closely associated. Here we describe the x-ray crystal structures of human ppGalNAcT-2 (hT2) bound to the product UDP at 2.75 A resolution and to UDP and an acceptor peptide substrate EA2 (PTTDSTTPAPTTK) at 1.64 A resolution. The conformations of both UDP and residues Arg362-Ser372 vary greatly between the two structures. In the hT2-UDP-EA2 complex, residues Arg362-Ser373 comprise a loop that forms a lid over UDP, sealing it in the active site, whereas in the hT2-UDP complex this loop is folded back, exposing UDP to bulk solvent. EA2 binds in a shallow groove with threonine 7 positioned consistent with in vitro data showing it to be the preferred site of glycosylation. The relative orientations of the hT2 catalytic and lectin domains differ dramatically from that of murine ppGalNAcT-1 and also vary considerably between the two hT2 complexes. Indeed, in the hT2-UDP-EA2 complex essentially no contact is made between the catalytic and lectin domains except for the peptide bridge between them. Thus, the hT2 structures reveal an unexpected flexibility between the catalytic and lectin domains and suggest a new mechanism used by hT2 to capture glycosylated substrates. Kinetic analysis of hT2 lacking the lectin domain confirmed the importance of this domain in acting on glycopeptide but not peptide substrates. The structure of the hT2-UDP-EA2 complex also resolves long standing questions regarding ppGalNAcT acceptor substrate specificity.

Selected figure(s)

Figure 3.
FIGURE 3. Hydrogen bonds and hydrophobic interactions mediating binding between hT2 and EA2. EA2 is shown as a stylized drawing with yellow carbon atoms, and the individual residues Ser^5–Lys^13 are labeled in red. Hydrogen bonds are shown by the blue dashed lines along with their corresponding lengths in Ångstroms. Hydrophobic interactions are shown by the red "eyelashes." Water molecules are shown as red spheres. The diagram was created by editing the output from the program Ligplot (47).

Figure 4.
FIGURE 4. Stereo view of EA2 binding to hT2. The transparent surface of hT2 is colored cyan, except for the surface of flexible loop residues Arg^362–Ser^372, which is colored yellow. A ribbon diagram of residues Arg^362–Ser^373 is shown in yellow. EA2 is shown with white carbons, and individual residues are indicated by white letter/number combinations. The side chains of hT2 residues interacting with EA2 are indicated by the black letter/number combinations. The five water molecules in the putative GalNAc binding pocket are shown as red spheres, only two of which are indicated for purposes of clarity. Two additional water molecules bound to shallow pockets in the EA2 cleft are also shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 8613-8619) copyright 2006.

Figures were selected by an automated process.