2dik: Difference between revisions
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|PDB= 2dik |SIZE=350|CAPTION= <scene name='initialview01'>2dik</scene>, resolution 2.5Å | |PDB= 2dik |SIZE=350|CAPTION= <scene name='initialview01'>2dik</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </span> | ||
|GENE= PPDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1512 Clostridium symbiosum]) | |GENE= PPDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1512 Clostridium symbiosum]) | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dik OCA], [http://www.ebi.ac.uk/pdbsum/2dik PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dik RCSB]</span> | |||
}} | }} | ||
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[[Category: Herzberg, O.]] | [[Category: Herzberg, O.]] | ||
[[Category: Huang, K.]] | [[Category: Huang, K.]] | ||
[[Category: kinase]] | [[Category: kinase]] | ||
[[Category: phosphotransferase]] | [[Category: phosphotransferase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:35:06 2008'' | ||
Revision as of 02:35, 31 March 2008
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| , resolution 2.5Å | |||||||
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| Ligands: | |||||||
| Gene: | PPDK (Clostridium symbiosum) | ||||||
| Activity: | Pyruvate, phosphate dikinase, with EC number 2.7.9.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE
OverviewOverview
Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of ATP, Pi, and pyruvate with AMP, PPi, and PEP in three partial reactions: (1) E + ATP --> E.ATP --> E-PP.AMP, (2) E-PP.AMP + Pi --> E-PP.AMP.Pi --> E-P.AMP.PPi, and (3) E-P + pyruvate --> E-P.pyruvate --> E.PEP. The Clostridium symbiosum PPDK structure consists of N-terminal, central, and C-terminal domains. The N-terminal and central domains catalyze partial reactions 1 and 2 whereas the C-terminal and central domains catalyze partial reaction 3. The goal of the present work is to determine where on the N-terminal domain catalysis of partial reactions 1 and 2 occurs and, in particular, where the Pi binding site is located. Computer modeling studies implicated Arg337 as a key residue for Pi binding. This role was tested by site-directed mutagenesis. The R337A PPDK was shown to be impaired in catalysis of the forward (kcat 300-fold lower) and reverse (kcat 30-fold lower) full reactions. Time courses for the single turnover reactions were measured to show that catalysis of partial reaction 1 is 5-fold slower in the mutant, catalysis of the second partial reaction is 140-fold slower in the mutant, and catalysis of the third partial reaction is unaffected. With the exception of the mutation site, the crystal structure of the R337A PPDK closely resembles the structure of the wild-type protein. Thus, the altered kinetic properties observed for this mutant are attributed solely to the elimination of the interaction between substrate and the guanidinium group of the Arg337 side chain. On the basis of these findings we propose that the Pi binding site is located within the crevice of the PPDK N-terminal domain, at a site that is flanked by the ATP beta-P and the Mg2+ cofactor.
About this StructureAbout this Structure
2DIK is a Single protein structure of sequence from Clostridium symbiosum. This structure supersedes the now removed PDB entry 1BUK. Full crystallographic information is available from OCA.
ReferenceReference
Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase., McGuire M, Huang K, Kapadia G, Herzberg O, Dunaway-Mariano D, Biochemistry. 1998 Sep 29;37(39):13463-74. PMID:9753432
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