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PDBsum entry 4ga5
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PDB id:
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Transferase
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Title:
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Crystal structure of amp phosphorylasE C-terminal deletion mutant in the apo-form
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Structure:
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Putative thymidine phosphorylase. Chain: b, a, c, d, e, f, g, h. Fragment: unp residues 1-493. Synonym: tdrpase. Engineered: yes
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Source:
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Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Gene: deoa. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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3.25Å
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R-factor:
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0.261
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R-free:
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0.289
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Authors:
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Y.Nishitani,R.Aono,A.Nakamura,T.Sato,H.Atomi,T.Imanaka,K.Miki
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Key ref:
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Y.Nishitani
et al.
(2013).
Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.
J Mol Biol,
425,
2709-2721.
PubMed id:
DOI:
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Date:
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25-Jul-12
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Release date:
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15-May-13
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PROCHECK
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Headers
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References
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Q5JCX3
(AMPPA_THEKO) -
AMP phosphorylase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
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Seq:
Struc:
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503 a.a.
493 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.2.4.2.57
- Amp phosphorylase.
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Reaction:
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1.
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AMP + phosphate = alpha-D-ribose 1,5-bisphosphate + adenine
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2.
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CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate
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3.
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UMP + phosphate = alpha-D-ribose 1,5-bisphosphate + uracil
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AMP
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+
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phosphate
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=
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alpha-D-ribose 1,5-bisphosphate
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+
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adenine
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CMP
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+
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phosphate
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=
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cytosine
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+
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alpha-D-ribose 1,5-bisphosphate
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UMP
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+
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phosphate
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=
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alpha-D-ribose 1,5-bisphosphate
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+
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uracil
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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J Mol Biol
425:2709-2721
(2013)
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PubMed id:
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Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.
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Y.Nishitani,
R.Aono,
A.Nakamura,
T.Sato,
H.Atomi,
T.Imanaka,
K.Miki.
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ABSTRACT
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AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP
metabolic pathway recently found in archaea, converting AMP and phosphate into
adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that
AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large
macromolecular structure (>40-mers) in solution. To investigate its unique
multimerization feature, we determined the first crystal structures of
Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two
truncated forms of Tk-AMPpase (Tk-AMPpaseΔN84 and Tk-AMPpaseΔC10) clarified
that this multimerization is achieved by two dimer interfaces within a single
molecule: one by the central domain and the other by the C-terminal domain,
which consists of an unexpected domain-swapping interaction. The N-terminal
domain, characteristic of archaeal enzymes, is essential for enzymatic activity,
participating in multimerization as well as domain closure of the active site
upon substrate binding. Moreover, biochemical analysis demonstrated that the
macromolecular assembly of Tk-AMPpase contributes to its high thermostability,
essential for an enzyme from a hyperthermophile. Our findings unveil a unique
archaeal nucleotide phosphorylase that is distinct in both function and
structure from previously known members of the nucleoside phosphorylase II
family.
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