PDBsum entry: 1jv1

Transferase

PDB id: 1jv1

Contents

Protein chains

490 a.a. *

Ligands

UD1 ×2

Waters ×842

* Residue conservation analysis

PDB id:

1jv1

Name:

Transferase

Title:

Crystal structure of human agx1 complexed with udpglcnac

Structure:

Glcnac1p uridyltransferase isoform 1: agx1. Chain: a, b. Synonym: udp-n-acetylglucosamine pyrophosphorylase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uap1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.183 R-free: 0.220

Authors:

C.Peneff,Y.Bourne

Key ref:

C.Peneff et al. (2001). Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. EMBO J, 20, 6191-6202. PubMed id: 11707391 DOI: 10.1093/emboj/20.22.6191

Date:

28-Aug-01 Release date: 28-Aug-02

Protein chains

Q16222  (UAP1_HUMAN) -  UDP-N-acetylhexosamine pyrophosphorylase

Seq: 522 a.a.

Struc: 490 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.23 - UDP-N-acetylglucosamine diphosphorylase.
• Pathway: UDP-N-acetylglucosamine Biosynthesis
• Reaction: UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N- acetyl-D-glucosamine

UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N- acetyl-D-glucosamine (Bound ligand (Het Group name = UD1) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (4 terms)
• Biological process: metabolic process (3 terms)
• Biochemical function: transferase activity (3 terms)

reference

DOI no: 10.1093/emboj/20.22.6191

EMBO J 20:6191-6202 (2001)

PubMed id: 11707391

Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture.

C.Peneff, P.Ferrari, V.Charrier, Y.Taburet, C.Monnier, V.Zamboni, J.Winter, M.Harnois, F.Fassy, Y.Bourne.

ABSTRACT

The recently published human genome with its relatively modest number of genes has highlighted the importance of post-transcriptional and post-translational modifications, such as alternative splicing or glycosylation, in generating the complexities of human biology. The human UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylases AGX1 and AGX2, which differ in sequence by an alternatively spliced 17 residue peptide, are key enzymes synthesizing UDPGlcNAc, an essential precursor for protein glycosylation. To better understand the catalytic mechanism of these enzymes and the role of the alternatively spliced segment, we have solved the crystal structures of AGX1 and AGX2 in complexes with UDPGlcNAc (at 1.9 and 2.4 A resolution, respectively) and UDPGalNAc (at 2.2 and 2.3 A resolution, respectively). Comparison with known structures classifies AGX1 and AGX2 as two new members of the SpsA-GnT I Core superfamily and, together with mutagenesis analysis, helps identify residues critical for catalysis. Most importantly, our combined structural and biochemical data provide evidence for a change in the oligomeric assembly accompanied by a significant modification of the active site architecture, a result suggesting that the two isoforms generated by alternative splicing may have distinct catalytic properties.

Selected figure(s)

Figure 3.
Figure 3 The AGX1 dimer. (A) Ribbon representation of the AGX1 dimer. Each subunit is coloured as in Figure 2A. One subunit is shown with a transparent molecular surface. The red arrows indicate the site of insertion of the 17 residue peptide in AGX2 in each subunit. (B) Stereo view of the AGX1 UDPGlcNAc-binding pocket of one subunit occluded by the I loop of the other subunit. I loop residues Lys455 and Arg453 (purple carbon atoms) are hydrogen-bonded to UDPGlcNAc phosphate groups. Arg115, which lies at the dimer interface, is shown under a transparent surface with orange carbon atoms. An asterisk indicates the site of insertion of the 17 residue peptide in AGX2. The protein surface corresponding to the central core and the N-terminal domains is coloured in beige and green, respectively.

Figure 4.
Figure 4 Structural alignment of the central domain of AGX1 and the Ppase domain of GlmU. Ribbon representations of the superimposed structures of the UDPGlcNAc-complexed forms of AGX1 and EcGlmU, which aligned with an r.m.s.d. of 1.8 Å over 180 C . AGX1 is coloured as in Figure 2A whilst GlmU is shown in cyan with bound UDPGlcNAc in green thin sticks and the NB loop highlighted in green.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6191-6202) copyright 2001.

Figures were selected by an automated process.