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BMB170a_2011_LECTURE8

BMB170a_2011_LECTURE8 - BMB/Bi/Ch170a,Proteins...

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Metalloproteins Enzymes Nucleo4de binding proteins BMB/Bi/Ch170a Proteins Lecture 8, Oct 20
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Metalloproteins Es4mated ~1/3 of all proteins contain metals Na, Mg, K, Ca V, Mn, Fe, Co, Ni, Cu, Zn Mo, Cd, W Metalloproteomics: Structural and func4onal annota4on of proteins in structural genomics Shi et al Structure (2005)13:1473 10S15% contain stoichiometric amounts of transi4on metals
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Role of metals in basic geobiochemical cycles Morel & Price Science (2003) 300:942 N cycle K, Mg 10 8 atoms/cell ~10 mM Ca, Zn, Fe 10 5 atoms/cell~ 0.1 mM Cu, Mn, Mo 10 4 atoms/cell~ 10 µM V, Co, Ni low abundance Finney & O’Halloran Science (2003) 300:931 in vivo metal concentra4ons (E. coli)
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Protein ligands Major ligands Cys, His, Asp, Glu Rarer examples Met (cytochrome c, azurin) Tyr (dioxygenase, catalase) Asn (Ca binding proteins, lipoxygenase) Gln (sub4lisin Ca, stellacyanin?) Ser (MoFeSprotein, ferredoxins, DMSO reductase) Lys (phosphoenolpyruvate carboxykinase) carbonyl O (Ca 2+ sites) amide N (P cluster/nitrile hydratase) amino N (cytochrome f, CooA (pro)) carboxy C (lipoxygenase), formyl Met (Mg of Bchl in LH2) Arg (bio4n synthase) Trp? no examples yet ; Trp as radical S cytc peroxidase
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tetrahedral octahedral trigonal bipyramid square planar Idealized coordina4on geometries Typical metalSligand distances for first row metals: M S O/N 2.0S2.1 Å M S S 2.3 Å His/Glu/Asp coord HN N N ε 2 N δ 1 HN N M M H preferred monoprotonated preferred in proteins (75%) preferred in peptides C O O C O O anti syn bidentate -1 -1 Smallest coordina4on mo4fs 3 res S sq planar S AScluster Carbon monoxide dehydrogenaseSaCoA (1mjg) 6 res S sq planar S Nitrile hydratase 14 res S TetrS some Zn fingers 12 res S Oct S calcium sites Harding Acta Cryst (2006) D62:678
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distribu4on of Zn S N His in high resolu4on protein structures (res < 1.6 Å), rela4ve to d = 2.00 Å observed in small molecule structures Zn S O distances in PDB structures with bidentate carboxylate ligands (both d < 3.00 Å) Distribu4on of metal ligand distances in protein structures Harding Acta Cryst (2006) D62:678
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Mg 2+ ? 2.78 2.11 2.12 2.12, 2.13 W 2.39 2.29 Aldehyde ferredoxin oxidoreductase Chan et al Science (1995) 267:1463 (1aor) Common components in protein solu4ons S ooen at high conc Ion M••O (Å) ion rad (Å) Favored coord num. Na + 2.42 0.95 6 Mg 2+ 2.07 0.65 6 K + 2.84 1.33 7S8 Ca 2+ 2.39 0.99 6S8 H 2 O ~2.8 4 Dis4nguishing Na + , Mg 2+ , K + , ( Ca 2+ ) from H 2 O ? Harding Acta Cryst (2006) D62:678
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Metal composi4on and quan4ta4on: ICPSMS (induc4vely coupled plasma S mass spectrometry) atomic absorp4on chemical methods Protein quan4ta4on protein S most difficult in prac4ce S colorimetric methods can be off by 100%+/S Nitrogenase FeMoScofactor S 1Mo:5S8Fe:6S9S (actual 1:7:9)
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