Database accession: MF7000566
Name: Nucleoside diphosphate sugar hydrolase (Bdellovibrio bacteriovorus)
PDB ID: 5c8l
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Bdellovibrio bacteriovorus
Primary publication of the structure:
de la Peña AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
(2015) PLoS ONE 10: e0141716
PMID: 26524597
Abstract:
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
ADP-ribose diphosphatase activity ADP-ribose diphosphatase activity
ADP-sugar diphosphatase activity ADP-sugar diphosphatase activity
bis(5'-adenosyl)-pentaphosphatase activity bis(5'-adenosyl)-pentaphosphatase activity
guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity
UDP-sugar diphosphatase activity UDP-sugar diphosphatase activity
Biological process:
nucleoside phosphate metabolic process nucleoside phosphate metabolic process
ribose phosphate metabolic process ribose phosphate metabolic process
Cellular component:
cytosol cytosol
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: ADP-ribose pyrophosphatase
Source organism: Bdellovibrio bacteriovorus
Length: 182 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKHLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGEFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEWN
UniProtKB AC: Q6MIH8 (positions: 1-182)
Coverage: 100%
Name: ADP-ribose pyrophosphatase
Source organism: Bdellovibrio bacteriovorus
Length: 182 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMKHLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGEFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEWN
UniProtKB AC: Q6MIH8 (positions: 3-181)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: NUDIX domain
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The authors claim that ADP-ribose pyrophosphatase forms a symmetric homodimer, wherein the two catalytic sites are formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition and catalytic activity (PMID:11323725). E. coli ADPRase elutes as a dimer in gel exclusion chromatography (PMID:11323725). The N-terminal subdomain (residues 1-54) mediates dimerization and is a strong candidate for MSF, while the C-terminal one is a folded Nudix domain. Other structures belonging to the same domain type also show features implying MSF: large relative interface, domain swapping and a lack of the monomeric form in gel filtration experiments (PMID:12906832, PMID:15210687).
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)
