2r5v
From Proteopedia
(New page: 200px {{Structure |PDB= 2r5v |SIZE=350|CAPTION= <scene name='initialview01'>2r5v</scene>, resolution 2.300Å |SITE= <scene name='pdbsite=AC1:Co+Binding+Site+...) |
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|PDB= 2r5v |SIZE=350|CAPTION= <scene name='initialview01'>2r5v</scene>, resolution 2.300Å | |PDB= 2r5v |SIZE=350|CAPTION= <scene name='initialview01'>2r5v</scene>, resolution 2.300Å | ||
|SITE= <scene name='pdbsite=AC1:Co+Binding+Site+For+Residue+A+4113'>AC1</scene>, <scene name='pdbsite=AC2:Co+Binding+Site+For+Residue+B+4114'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+B+4115'>AC3</scene>, <scene name='pdbsite=AC4:Hhh+Binding+Site+For+Residue+B+4116'>AC4</scene> and <scene name='pdbsite=AC5:Hhh+Binding+Site+For+Residue+A+4114'>AC5</scene> | |SITE= <scene name='pdbsite=AC1:Co+Binding+Site+For+Residue+A+4113'>AC1</scene>, <scene name='pdbsite=AC2:Co+Binding+Site+For+Residue+B+4114'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+B+4115'>AC3</scene>, <scene name='pdbsite=AC4:Hhh+Binding+Site+For+Residue+B+4116'>AC4</scene> and <scene name='pdbsite=AC5:Hhh+Binding+Site+For+Residue+A+4114'>AC5</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HHH:(2S)-HYDROXY(4-HYDROXYPHENYL)ETHANOIC+ACID'>HHH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/4-hydroxymandelate_synthase 4-hydroxymandelate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.46 1.13.11.46] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxymandelate_synthase 4-hydroxymandelate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.46 1.13.11.46] </span> |
|GENE= HmaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 Amycolatopsis orientalis]) | |GENE= HmaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 Amycolatopsis orientalis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5v OCA], [http://www.ebi.ac.uk/pdbsum/2r5v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2r5v RCSB]</span> | ||
}} | }} | ||
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[[Category: He, P.]] | [[Category: He, P.]] | ||
[[Category: Moran, G R.]] | [[Category: Moran, G R.]] | ||
| - | [[Category: CO]] | ||
| - | [[Category: HHH]] | ||
| - | [[Category: PO4]] | ||
[[Category: dioxygenase]] | [[Category: dioxygenase]] | ||
[[Category: non-heme iron]] | [[Category: non-heme iron]] | ||
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[[Category: vancomycin]] | [[Category: vancomycin]] | ||
| - | ''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 04:56:53 2008'' |
Revision as of 01:56, 31 March 2008
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| , resolution 2.300Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , and | ||||||
| Ligands: | , , | ||||||
| Gene: | HmaS (Amycolatopsis orientalis) | ||||||
| Activity: | 4-hydroxymandelate synthase, with EC number 1.13.11.46 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Hydroxymandelate Synthase Crystal Structure
Overview
The crystal structure of the hydroxymandelate synthase (HMS).Co2+.hydroxymandelate (HMA) complex determined to a resolution of 2.3 A reveals an overall fold that consists of two similar beta-barrel domains, one of which contains the characteristic His/His/acid metal-coordination motif (facial triad) found in the majority of Fe2+-dependent oxygenases. The fold of the alpha-carbon backbone closely resembles that of the evolutionarily related enzyme 4-hydroxyphenylpyruvate dioxygenase (HPPD) in its closed conformation with a root-mean-square deviation of 1.85 A. HPPD uses the same substrates as HMS but forms instead homogentisate (HG). The active site of HMS is significantly smaller than that observed in HPPD, reflecting the relative changes in shape that occur in the conversion of the common HPP substrate to the respective HMA or HG products. The HMA benzylic hydroxyl and carboxylate oxygens coordinate to the Co2+ ion, and three other potential H-bonding interactions to active site residue side chains are observed. Additionally, it is noted that there is a buried well-ordered water molecule 3.2 A from the distal carboxylate oxygen. The p-hydroxyl group of HMA is within hydrogen-bonding distance of the side chain hydroxyl of a serine residue (Ser201) that is conserved in both HMS and HPPD. This potential hydrogen bond and the known geometry of iron ligation for the substrate allowed us to model 4-hydroxyphenylpyruvate (HPP) in the active sites of both HMS and HPPD. These models suggest that the position of the HPP substrate differs between the two enzymes. In HMS, HPP binds analogously to HMA, while in HPPD, the p-hydroxyl group of HPP acts as a hydrogen-bond donor and acceptor to Ser201 and Asn216, respectively. It is suggested that this difference in the ring orientation of the substrate and the corresponding intermediates influences the site of hydroxylation.
About this Structure
2R5V is a Single protein structure of sequence from Amycolatopsis orientalis. Full crystallographic information is available from OCA.
Reference
Two roads diverged: the structure of hydroxymandelate synthase from Amycolatopsis orientalis in complex with 4-hydroxymandelate., Brownlee J, He P, Moran GR, Harrison DH, Biochemistry. 2008 Feb 19;47(7):2002-13. Epub 2008 Jan 24. PMID:18215022
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