PDBsum entry: 1tz6

Transferase

PDB id: 1tz6

Contents

Protein chains

297 a.a. *

Ligands

ACP ×2

AIS

Metals

_MG ×2

__K ×4

Waters ×57

* Residue conservation analysis

PDB id:

1tz6

Name:

Transferase

Title:

Crystal structure of aminoimidazole riboside kinase from salmonella enterica complexed with aminoimidazole riboside and atp analog

Structure:

Putative sugar kinase. Chain: a, b. Engineered: yes

Source:

Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: ct18. Gene: stm4066. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.217 R-free: 0.285

Authors:

Y.Zhang,M.Dougherty,D.M.Downs,S.E.Ealick

Key ref:

Y.Zhang et al. (2004). Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily. Structure, 12, 1809-1821. PubMed id: 15458630 DOI: 10.1016/j.str.2004.07.020

Date:

09-Jul-04 Release date: 12-Oct-04

Protein chains

Q8ZKR2  (Q8ZKR2_SALTY) -  Putative sugar kinase

Seq: 319 a.a.

Struc: 297 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.1.4 - Fructokinase.
• Reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate

ATP + D-fructose (Bound ligand (Het Group name = AIS) matches with 50.00% similarity) = ADP (Bound ligand (Het Group name = ACP) matches with 81.00% similarity) + D-fructose 6-phosphate

• Enzyme class 2: E.C.3.6.1.26 - CDP-diacylglycerol diphosphatase.
• Reaction: CDP-diacylglycerol + H₂O = CMP + phosphatidate

CDP-diacylglycerol + H(2)O = CMP (Bound ligand (Het Group name = ACP) matches with 62.00% similarity) + phosphatidate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biological process: D-ribose metabolic process (1 term)
• Biochemical function: transferase activity (6 terms)

reference

DOI no: 10.1016/j.str.2004.07.020

Structure 12:1809-1821 (2004)

PubMed id: 15458630

Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily.

Y.Zhang, M.Dougherty, D.M.Downs, S.E.Ealick.

ABSTRACT

The crystal structures of a Salmonella enterica aminoimidazole riboside (AIRs) kinase, its complex with the substrate AIRs, and its complex with AIRs and an ATP analog were determined at 2.6 angstroms, 2.9 angstroms, and 2.7 angstroms, respectively. The product of the Salmonella-specific gene stm4066, AIRs kinase, is a homodimer with one active site per monomer. The core structure, consisting of an eight-stranded beta sheet flanked by eight alpha helices, indicates that AIRs kinase is a member of the ribokinase superfamily. Unlike ribokinase and adenosine kinase in this superfamily, AIRs kinase does not show significant conformational changes upon substrate binding. The active site is covered by a lid formed by residues 16-28 and 86-100. A comparison of the structure of AIRs kinase with other ribokinase superfamily members suggests that the active site lid and conformational changes that occur upon substrate binding may be advanced features in the evolution of the ribokinase superfamily.

Selected figure(s)

Figure 2.
Figure 2. The Active Site of AIRs Kinase(A) Electron density of AIRs and AMP-PCP. The F[o] - F[c] omit map was calculated to 2.7 Å after one cycle of refinement without AIRs and AMP-PCP from the model (bluegreen mesh, contoured at 3s). AIRs and AMP-PCP are drawn in ball-and-stick representations. Prepared using BOBSCRIPT (Esnouf, 1997).(B) A schematic drawing of the active site. Key hydrogen bonds are indicated by dashed lines with the corresponding donor-acceptor distance labeled.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1809-1821) copyright 2004.

Figure was selected by an automated process.