3I7V

Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5

Replaces:  2PQ1

Summary for 3I7V

• Entry DOI: 10.2210/pdb3i7v/pdb
• Related: 3I7U
• Descriptor: AP4A hydrolase, ADENOSINE-5'-TRIPHOSPHATE, BIS(ADENOSINE)-5'-TETRAPHOSPHATE, ... (6 entities in total)
• Functional Keywords: nudix protein, diadenosine polyphosphate, ap4a, hydrolase, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• Biological source: Aquifex aeolicus Vf5
• Total number of polymer chains: 2
• Total formula weight: 34040.30

Authors

Jeyakanthan, J.,Kanaujia, S.P.,Nakagawa, N.,Sekar, K.,Kuramitsu, S.,Shinkai, A.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2009-07-09, release date: 2009-07-21, Last modification date: 2023-11-01)

Primary citation

Jeyakanthan, J.,Kanaujia, S.P.,Nishida, Y.,Nakagawa, N.,Praveen, S.,Shinkai, A.,Kuramitsu, S.,Yokoyama, S.,Sekar, K.
Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5
Acta Crystallogr.,Sect.D, 66:116-124, 2010

PubMed Abstract: Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

PubMed: 20124691
DOI: 10.1107/S0907444909047064

Experimental method

X-RAY DIFFRACTION (1.95 Å)