General Information

Database accession: MF7000059

Name: ADPR-ase/AMPCPR complex

PDB ID: 1khz PDBe

Experimental method: X-ray (2.04 Å)

Assembly: Homodimer

Source organism: Escherichia coli

Primary publication of the structure:

Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
(2002) Biochemistry 41: 9279-85

PMID: 12135348 PubMed

Abstract:

Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.


Function and Biology 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 GeneOntology

ADP-sugar diphosphatase activity ADP-sugar diphosphatase activity GeneOntology

magnesium ion binding magnesium ion binding GeneOntology

protein homodimerization activity protein homodimerization activity GeneOntology

pyrophosphatase activity pyrophosphatase activity GeneOntology

Biological process:

nucleoside phosphate metabolic process nucleoside phosphate metabolic process GeneOntology

response to heat response to heat GeneOntology

ribose phosphate metabolic process ribose phosphate metabolic process GeneOntology

Cellular component:

cytosol cytosol GeneOntology

Structure Summary 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


Chain A

Name: ADP-ribose pyrophosphatase

Source organism: Escherichia coli

Length: 209 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA

UniProtKB AC: Q93K97 (positions: 1-209) UniProt

Coverage: 100%

Chain B

Name: ADP-ribose pyrophosphatase

Source organism: Escherichia coli

Length: 209 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMLKPDNLPVTFGKNDVEIIARETLYRGFFSLDLYRFRHRLFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLIEQIRIAAYDTSETPWLLEMVAGMIEEGESVEDVARREAIEEAGLIVKRTKPVLSFLASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHHQALKNEWA

UniProtKB AC: Q93K97 (positions: 8-209) UniProt

Coverage: 96%

Evidence 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:

Related Structure(s) 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).

There are 38 related structures in the MFIB database:






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