PDBsum entry 1vk3

Ligase

PDB id: 1vk3

Contents

Protein chain

586 a.a. *

Metals

_CL

Waters ×221

* Residue conservation analysis

PDB id:

1vk3

Name:

Ligase

Title:

Crystal structure of phosphoribosylformylglycinamidine synthase ii (tm1246) from thermotoga maritima at 2.15 a resolution

Structure:

Phosphoribosylformylglycinamidine synthase ii. Chain: a. Synonym: fgam synthase ii. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: purl, tm1246. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.15Å R-factor: 0.190 R-free: 0.254

Authors:

Joint Center For Structural Genomics (Jcsg)

Key ref:

I.I.Mathews et al. (2006). Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. Proteins, 63, 1106-1111. PubMed id: 16544324 DOI: 10.1002/prot.20650

Date:

23-Apr-04 Release date: 11-May-04

Protein chain

Q9X0X3  (PURL_THEMA) -  Phosphoribosylformylglycinamidine synthase subunit PurL from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 603 a.a.

Struc: 586 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.5.3 - phosphoribosylformylglycinamidine synthase.
• Pathway: Purine Biosynthesis (early stages)
• Reaction: N₂-formyl-N₁-(5-phospho-beta-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-formamido-N₁-(5-O-phospho-beta-D-ribosyl)acetamidine + L-glutamate + ADP + phosphate + H⁺

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

reference

DOI no: 10.1002/prot.20650

Proteins 63:1106-1111 (2006)

PubMed id: 16544324

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.

I.I.Mathews, S.S.Krishna, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, L.Jaroszewski, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, K.Quijano, R.Reyes, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 2.
Figure 2. Domain arrangement and structural alignment of smPurL and lgPurL. A: Domain arrangement of PurM, ThiL, smPurL, and lgPurL proteins. PurM and ThiL are homodimers. smPurL (gray) and the central domain of lgPurL (blue) have the same domain arrangement as a PurM dimer. lgPurL has two additional domains as compared with smPurL. The N-terminal domain homologous to the PurS protein is colored green and the C-terminal glutaminase domain is colored red. B: Stereo ribbon diagram of a superposition of smPurL (gray) and residues 183-960 of lgPurL from S. typhimurium (blue). The lgPurL N-terminal domain of unknown function and the C-terminal glutaminase domain are colored green and red, respectively. These extra domains of lgPurL correspond to the PurS (TM1244) and PurQ (TM1245) proteins in T. maritima. The structures were aligned using the DALI server.

Figure 3.
Figure 3. A: Stereo diagram of a close-up of the putative active site of TM1246 superimposed on the lgPurL structure shown in ribbon representation. The sulfate ions are from the lgPurL structure. The start and end regions of the glycine-rich loop in both the structures are labeled in red. B: Stereo diagram of a close-up of the lgPurL ADP-binding site superimposed on the smPurL structure shown in ribbon representation. The ADP moiety and Mg^2+ ions are from the lgPurL structure. In A and B, residues are numbered according to TM1246 structure (PDB 1vk3) and the equivalent residues of lgPurL (PDB 1t3t) are shown in parentheses.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 1106-1111) copyright 2006.

Figures were selected by an automated process.