Database accession: MF7000578
Name: ADP ribose pyrophosphatase (Thermus thermophilus HB8)
PDB ID: 3x0n
Experimental method: X-ray (1.12 Å)
Assembly: Homodimer
Source organism: Thermus thermophilus
Primary publication of the structure:
Furuike Y, Akita Y, Miyahara I, Kamiya N
ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors.
(2016) Biochemistry 55: 1801-12
PMID: 26979298
Abstract:
Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn(2+), Zn(2+), or Mg(2+) as cofactors. Here, we report the reaction pathway observed in the catalytic center of TtADPRase, based on cryo-trapping X-ray crystallography at atomic resolutions around 1.0 Å using Mn(2+) as the reaction trigger, which was soaked into TtADPRase-ADPR binary complex crystals. Integrating 11 structures along the reaction timeline, five reaction states of TtADPRase were assigned, which were ADPRase alone (E), the ADPRase-ADPR binary complex (ES), two ADPRase-ADPR-Mn(2+) reaction intermediates (ESM, ESMM), and the postreaction state (E'). Two Mn(2+) ions were inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states. The ADPR-hydrolysis reaction was characterized by electrostatic, proximity, and orientation effects, and by preferential binding for the transition state. A new reaction mechanism is proposed, which differs from previous ones suggested from structure analyses with nonhydrolyzable substrate analogues or point-mutated ADPRases.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
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
metal ion binding metal ion binding
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, A-2
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: Thermus thermophilus
Length: 170 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGRVYYGGVERTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRELAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEAHPDEDEAIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLRGR
UniProtKB AC: Q5SKW5 (positions: 10-168)
Coverage: 93%
Name: ADP-ribose pyrophosphatase
Source organism: Thermus thermophilus
Length: 170 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGRVYYGGVERTYLYRGRILNLALEGRYEIVEHKPAVAVIALREGRMLFVRQMRPAVGLAPLEIPAGLIEPGEDPLEAARRELAEETGLSGDLTYLFSYFVSPGFTDEKTHVFLAENLKEVEAHPDEDEAIEVVWMRPEEALERHQRGEVEFSATGLVGVLYYHAFLRGR
UniProtKB AC: Q5SKW5 (positions: 10-168)
Coverage: 93%
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 A-2:
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)
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