1pp9: Difference between revisions

← Older edit Newer edit →

Revision as of 23:02, 30 March 2008

File:1pp9.gif

, resolution 2.10Å

Ligands:

, , , , , , , , , ,

Activity:

Ubiquinol--cytochrome-c reductase, with EC number 1.10.2.2

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Bovine cytochrome bc1 complex with stigmatellin bound

OverviewOverview

Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alphaA helix.

About this StructureAbout this Structure

1PP9 is a Protein complex structure of sequences from Bos taurus. Full crystallographic information is available from OCA.

ReferenceReference

Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern., Huang LS, Cobessi D, Tung EY, Berry EA, J Mol Biol. 2005 Aug 19;351(3):573-97. PMID:16024040

Page seeded by OCA on Sun Mar 30 23:02:40 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 4: / Line 4: @@
 |PDB= 1pp9 |SIZE=350|CAPTION= <scene name='initialview01'>1pp9</scene>, resolution 2.10&Aring;
 |SITE=
-|LIGAND= <scene name='pdbligand=BHG:2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>BHG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</scene>, <scene name='pdbligand=UQ:UBIQUINONE-10'>UQ</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=PEE:PHOSPHATIDYLETHANOLAMINE'>PEE</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+|LIGAND= <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BHG:2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>BHG</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEE:PHOSPHATIDYLETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SMA:STIGMATELLIN+A'>SMA</scene>, <scene name='pdbligand=UQ:UBIQUINONE-10'>UQ</scene>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Ubiquinol--cytochrome-c_reductase Ubiquinol--cytochrome-c reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.2.2 1.10.2.2]
+|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquinol--cytochrome-c_reductase Ubiquinol--cytochrome-c reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.2.2 1.10.2.2] </span>
 |GENE=
+|DOMAIN=
+|RELATEDENTRY=
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pp9 OCA], [http://www.ebi.ac.uk/pdbsum/1pp9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pp9 RCSB]</span>
 }}
@@ Line 27: / Line 30: @@
 [[Category: Huang, L S.]]
 [[Category: Tung, E Y.]]
-[[Category: AZI]]
-[[Category: BHG]]
-[[Category: CDL]]
-[[Category: FES]]
-[[Category: GOL]]
-[[Category: HEC]]
-[[Category: HEM]]
-[[Category: PEE]]
-[[Category: PO4]]
-[[Category: SMA]]
-[[Category: UQ]]
 [[Category: complex iii]]
 [[Category: cytochrome b]]
@@ Line 52: / Line 44: @@
 [[Category: stigmatellin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:27:13 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:02:40 2008''