1jcy: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1jcy.gif|left|200px]] | [[Image:1jcy.gif|left|200px]] | ||
'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium''' | {{Structure | ||
|PDB= 1jcy |SIZE=350|CAPTION= <scene name='initialview01'>1jcy</scene>, resolution 1.90Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> and <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] | |||
|GENE= | |||
}} | |||
'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1JCY is a [ | 1JCY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA]. | ||
==Reference== | ==Reference== | ||
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:[http:// | Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11747443 11747443] | ||
[[Category: 3-deoxy-8-phosphooctulonate synthase]] | [[Category: 3-deoxy-8-phosphooctulonate synthase]] | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
| Line 25: | Line 34: | ||
[[Category: kdo]] | [[Category: kdo]] | ||
[[Category: kdo8p]] | [[Category: kdo8p]] | ||
[[Category: | [[Category: kdo8p]] | ||
[[Category: pep]] | [[Category: pep]] | ||
[[Category: r5p]] | [[Category: r5p]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:01:42 2008'' | ||
Revision as of 10:01, 20 March 2008
| |||||||||||||
| 1jcy, resolution 1.90Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | R5P, CD, PO4 and PEP | ||||||||||||
| Activity: | 3-deoxy-8-phosphooctulonate synthase, with EC number 2.5.1.55 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium
Overview
We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.
About this Structure
1JCY is a Single protein structure of sequence from Aquifex aeolicus. Full crystallographic information is available from OCA.
Reference
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:11747443
Page seeded by OCA on Thu Mar 20 12:01:42 2008
