PDBsum entry 1vkm

Biosynthetic protein

PDB id: 1vkm

Contents

Protein chains

(+ 0 more) 292 a.a. *

Ligands

UNL ×6

EDO ×11

Metals

_MN ×16

Waters ×987

* Residue conservation analysis

PDB id:

1vkm

Name:

Biosynthetic protein

Title:

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 a resolution

Structure:

Conserved hypothetical protein tm1464. Chain: a, b, c, d, e, f. Engineered: yes. Other_details: possibly involved in carbohydrate metabolism

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1464. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.90Å R-factor: 0.156 R-free: 0.200

Authors:

Joint Center For Structural Genomics (Jcsg)

Key ref:

I.Levin et al. (2005). Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold. Proteins, 59, 864-868. PubMed id: 15822122 DOI: 10.1002/prot.20420

Date:

09-Jun-04 Release date: 29-Jun-04

Protein chains

Q9X1H5  (PSUG_THEMA) -  Pseudouridine-5'-phosphate glycosidase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 285 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.1.70 - pseudouridylate synthase.
• Reaction: D-ribose 5-phosphate + uracil = psi-UMP + H2O

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

Added reference

DOI no: 10.1002/prot.20420

Proteins 59:864-868 (2005)

PubMed id: 15822122

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.

I.Levin, M.D.Miller, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, T.Biorac, J.Cambell, 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, M.Hornsby, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of TM1464. (A) Stereo ribbon diagram of T. maritima TM1464 color-coded from N-terminus (blue) to C-terminus (red), showing the domain organization. Helices H1-H12, and -strands ( 1- 11) are indicated. (B) Diagram showing the secondary structure elements in TM1464 superimposed on its primary sequence. The -helices, 3[10]-helices, -bulges, and -turns are indicated. The -sheet strands are indicated by a red A, and -hairpins are depicted as red loops.

Figure 2.
Figure 2. (A) The TM1464 trimer viewed along the 3-fold axis. One subunit is shown in blue. The 3 UNLs bound to the putative active sites are shown as red spheres. (B) TM1464 shown in surface representation illustrating the narrow active site pocket, with the bound UNL in ball-and-stick configuration. (C) Close-up of the putative active site. TM1464 is shown in ribbon representation with the UNL, manganese, and interacting residues and waters in ball-and-stick configuration (see text). A SigmaA-weighted Fo-Fc omit map contoured at 3.0 is shown for the UNL, manganese, and coordinating waters. Putative H-bond interactions between the UNL and the protein are shown in yellow dotted lines.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 59, 864-868) copyright 2005.