Database accession: MF7000911
Name: H49N, H51N double mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase with TDP (Aneurinibacillus thermoaerophilus)
PDB ID: 2pam
Experimental method: X-ray (2.50 Å)
Assembly: Homodimer
Source organism: Aneurinibacillus thermoaerophilus
Primary publication of the structure:
Davis ML, Thoden JB, Holden HM
The x-ray structure of dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase.
(2007) J. Biol. Chem. 282: 19227-36
PMID: 17459872
Abstract:
The repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus L420-91(T) is composed of four alpha-d-rhamnose molecules and two 3-acetamido-3,6-dideoxy-alpha-d-galactose moieties (abbreviated as Fucp3NAc). Formation of the glycan layer requires nucleotide-activated sugars as the donor molecules. Whereas the enzymes involved in the synthesis of GDP-rhamnose have been well characterized, less is known regarding the structures and enzymatic mechanisms of the enzymes required for the production of dTDP-Fucp3NAc. One of the enzymes involved in the biosynthesis of dTDP-Fucp3NAc is a 3,4-ketoisomerase, hereafter referred to as FdtA. Here we describe the first three-dimensional structure of this sugar isomerase complexed with dTDP and solved to 1.5 A resolution. The FdtA dimer assumes an almost jellyfish-like appearance with the sole alpha-helices representing the tentacles. Formation of the FdtA dimer represents a classical example of domain swapping whereby beta-strands 2 and 3 from one subunit form part of a beta-sheet in the second subunit. The active site architecture of FdtA is characterized by a cluster of three histidine residues, two of which, His(49) and His(51), appear to be strictly conserved in the amino acid sequences deposited to date. Site-directed mutagenesis experiments, enzymatic assays, and x-ray crystallographic analyses suggest that His(49) functions as an active site base.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
isomerase activity isomerase activity
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase
Source organism: Aneurinibacillus thermoaerophilus
Length: 139 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLEKEG
UniProtKB AC: Q6T1W8 (positions: 2-136)
Coverage: 97%
Name: TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase
Source organism: Aneurinibacillus thermoaerophilus
Length: 139 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLEKEG
UniProtKB AC: Q6T1W8 (positions: 2-135)
Coverage: 96%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: WxcM-like, C-terminal
Evidence level: Insufficient evidence (candidate)
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Domain-swapped dimer with extensive subunit-subunit interface mainly contributed by beta sheet augmentation (PMID:17459872).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
