PDBsum entry: 1l4u

Transferase

PDB id: 1l4u

Contents

Protein chain

165 a.a. *

Ligands

ADP

EPE

Metals

_PT

_MG

_CL ×6

Waters ×194

* Residue conservation analysis

PDB id:

1l4u

Name:

Transferase

Title:

Crystal structure of shikimate kinase from mycobacterium tuberculosis in complex with mgadp and pt(ii) at 1.8 angstrom resolution

Structure:

Shikimate kinase. Chain: a. Synonym: sk. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: arok. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.221 R-free: 0.249

Authors:

Y.Gu,L.Reshetnikova,Y.Li,Y.Wu,H.Yan,S.Singh,X.Ji

Key ref:

Y.Gu et al. (2002). Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. J Mol Biol, 319, 779-789. PubMed id: 12054870 DOI: 10.1016/S0022-2836(02)00339-X

Date:

05-Mar-02 Release date: 12-Jun-02

Protein chain

P0A4Z2  (AROK_MYCTU) -  Shikimate kinase

Seq: 176 a.a.

Struc: 165 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.71 - Shikimate kinase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: ATP + shikimate = ADP + shikimate 3-phosphate

ATP + shikimate = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + shikimate 3-phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: growth (3 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1016/S0022-2836(02)00339-X

J Mol Biol 319:779-789 (2002)

PubMed id: 12054870

Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.

Y.Gu, L.Reshetnikova, Y.Li, Y.Wu, H.Yan, S.Singh, X.Ji.

ABSTRACT

Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing non-toxic antimicrobial agents, herbicides, and anti-parasite drugs, because the pathway is essential in the above species but is absent from mammals. The crystal structure of Mycobacterium tuberculosis SK (MtSK) in complex with MgADP has been determined at 1.8 A resolution, revealing critical information for the structure-based design of novel anti-M. tuberculosis agents. MtSK, with a five-stranded parallel beta-sheet flanked by eight alpha-helices, has three domains: the CORE domain, the shikimate-binding domain (SB), and the LID domain. The ADP molecule is bound with its adenine moiety sandwiched between the side-chains of Arg110 and Pro155, its beta-phosphate group in the P-loop, and the alpha and beta-phosphate groups hydrogen bonded to the guanidinium group of Arg117. Arg117 is located in the LID domain, is strictly conserved in SK sequences, is observed for the first time to interact with any bound nucleotide, and appears to be important in both substrate binding and catalysis. The crystal structure of MtSK (this work) and that of Erwinia chrysanthemi SK suggest a concerted conformational change of the LID and SB domains upon nucleotide binding.

Selected figure(s)

Figure 2.
Figure 2. Overall structure and representative electron density from MAD phasing of the MtSK·MgADP com- plex. MtSK contains eight a-helices (blue ribbons), five b-strands (yellow arrows), and two 310 helices (blue rib- bons) in three domains: LID, CORE, and SB. The LID domain starts from the C terminus of a6 and ends at the N terminus of a7; the SB domain consists of a2, a3, and the N-terminal half of a4; and the CORE domain contains the central five-stranded parallel b-sheet flanked with helices. ADP and Hepes are shown as ball- and-stick models with atomic color scheme (C, black; N, blue; O, red; S, yellow; and P, purple) and the Mg 2⁺ and Pt 2⁺ are shown as bigger purple spheres. The initial elec- tron density from MAD phasing is illustrated as green nets and contoured at the level of 1.0s for Mg 2⁺ , Pt 2⁺ , ADP, Hepes, and Arg117. The illustration was prepared using BOBSCRIPT. 38

Figure 4.
Figure 4. Mg 2⁺ coordination and ADP --protein inter- actions. The native structure of MtSK·MgADP reveals a typical six-coordinated Mg 2⁺ , which is illustrated by six continuous lines and highlighted by a green net: the final 2Fo 2 Fc electron density contoured at 1.0s. ADP is bound in the cavity that is constructed by the adenine- binding loop (residues 148 -- 155, not shown), P-loop (residues 9-- 17, blue loop in the middle), and residue Arg117 from the LID domain (residues 112 -- 124, yellow loop on the left). Broken lines represent hydrogen bonds. The Figure was prepared with BOBSCRIPT. 38

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 779-789) copyright 2002.

Figures were selected by the author.