PDBsum entry 2afb

Transferase

PDB id: 2afb

Contents

Protein chains

329 a.a. *

Metals

_CA ×4

_NI ×6

Waters ×394

* Residue conservation analysis

PDB id:

2afb

Name:

Transferase

Title:

Crystal structure of 2-dehydro-3- deoxygluconokinase (ec 2.7.1.45) (tm0067) from thermotoga maritima at 2.05 a resolution

Structure:

2-keto-3-deoxygluconate kinase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm0067. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.05Å R-factor: 0.177 R-free: 0.230

Authors:

Joint Center For Structural Genomics (Jcsg)

Key ref:

I.I.Mathews et al. (2008). Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution. Proteins, 70, 603-608. PubMed id: 18004772 DOI: 10.1002/prot.21842

Date:

25-Jul-05 Release date: 14-Feb-06

Supersedes:

1j5v

Protein chains

Q9WXS2  (Q9WXS2_THEMA) -  2-keto-3-deoxygluconate kinase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 339 a.a.

Struc: 329 a.a.

DOI no: 10.1002/prot.21842

Proteins 70:603-608 (2008)

PubMed id: 18004772

Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.

I.I.Mathews, D.McMullan, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.McPhillips, A.T.Morse, K.Quijano, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.van den Bedem, D.Weekes, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of TM0067. (A) Ribbon diagram of TM0067 color-coded according to domains I (light blue), II (orange), and III (green). Helices (H1-H14) and -strands ( 1- 14) are labeled. The arrow indicates the location of the putative active site by homology with T. thermophilus [see Fig. 2(A)]. The N- and C-termini are labeled, and -sheets A and B are labeled in red. (B) Diagram showing the secondary structural elements in TM0067 superimposed on its primary sequence. Helices are labeled H1-H14. The -hairpins are depicted as red loops, and the -turns and -turns are indicated. The -strands from -sheet A are labeled with a red A, while those from -sheet B are labeled with a red B. Disordered regions are represented by dashed lines.

Figure 2.
Figure 2. Structural analysis of 2-keto-3-deoxygluconate kinase. (A) Stereo diagram of a structural alignment of TM0067 (blue) and 2-keto-3-deoxygluconate kinase from T. thermophilus (PDB: 1v1a, grey), with bound ADP and 2-keto-3-deoxygluconate (KDG) shown as spheres. (B) Stereo view of the active site, with ADP, KDG, and the interacting residues shown in sticks. Carbon atoms are colored light blue (TM0067), grey (T. thermophilus enzyme), or yellow (ADP and KDG). Nitrogen, oxygen, and phosphorus atoms are colored blue, red, and orange, respectively. TM0067 residues are labeled; corresponding residues in T. thermophilus are in parentheses. (C) Ribbon diagram of the TM0067 hexamer. TM0067 forms a trimer of dimers, where the flap region is shared between the monomers of each dimer. In each dimer, one of the monomers is colored, while the other is in grey.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 603-608) copyright 2008.