This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1fyd
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1fyd |SIZE=350|CAPTION= <scene name='initialview01'>1fyd</scene>, resolution 2.25Å | |PDB= 1fyd |SIZE=350|CAPTION= <scene name='initialview01'>1fyd</scene>, resolution 2.25Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1ee1|1EE1]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fyd OCA], [http://www.ebi.ac.uk/pdbsum/1fyd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fyd RCSB]</span> | ||
}} | }} | ||
| Line 31: | Line 34: | ||
[[Category: Singh, R.]] | [[Category: Singh, R.]] | ||
[[Category: Symersky, J.]] | [[Category: Symersky, J.]] | ||
| - | [[Category: AMP]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: POP]] | ||
[[Category: amidotransferase]] | [[Category: amidotransferase]] | ||
[[Category: atp]] | [[Category: atp]] | ||
| Line 40: | Line 40: | ||
[[Category: pyrophosphatase]] | [[Category: pyrophosphatase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:32:39 2008'' |
Revision as of 17:32, 30 March 2008
| |||||||
| , resolution 2.25Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | NAD(+) synthase (glutamine-hydrolyzing), with EC number 6.3.5.1 | ||||||
| Related: | 1EE1
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION
Overview
The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).
About this Structure
1FYD is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis., Devedjiev Y, Symersky J, Singh R, Jedrzejas M, Brouillette C, Brouillette W, Muccio D, Chattopadhyay D, DeLucas L, Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):806-12. Epub 2001, May 25. PMID:11375500
Page seeded by OCA on Sun Mar 30 20:32:39 2008
