Journal:Acta Cryst D:S2059798319000676
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<scene name='80/806393/Cv/5'>A Ribbon diagram of PCPdr monomer</scene> (spectrum color) is shown in cartoon with pG bound to the active site shown in magenta ball-and-sticks. Briefly, the monomeric structure of PCPdr consists of a single α/β fold in which a twisted seven-stranded mixed β-sheet (β1-β5, β8, and β9) is flanked by two α helices on one side (α2, and α4) and three α helices (α1, α3, and α6) on other side. The active site is entirely formed by residues from only one monomeric subunit. It is located at the depression which is formed by the protruding loops of the α/β core of the protein. These loops are <scene name='80/806393/Cv/6'>loop-A (residues 9-19), loop-B (residues 85-112) and loop-C (residues 178-192)</scene> which could play an important role in substrate entry. The residues of <scene name='80/806393/Cv/7'>the catalytic triad, Cys144, Glu81 and His169</scene>, are located at the N-terminus of helix α4, C-terminus of strand β5 and C-terminus of strand β11, respectively. | <scene name='80/806393/Cv/5'>A Ribbon diagram of PCPdr monomer</scene> (spectrum color) is shown in cartoon with pG bound to the active site shown in magenta ball-and-sticks. Briefly, the monomeric structure of PCPdr consists of a single α/β fold in which a twisted seven-stranded mixed β-sheet (β1-β5, β8, and β9) is flanked by two α helices on one side (α2, and α4) and three α helices (α1, α3, and α6) on other side. The active site is entirely formed by residues from only one monomeric subunit. It is located at the depression which is formed by the protruding loops of the α/β core of the protein. These loops are <scene name='80/806393/Cv/6'>loop-A (residues 9-19), loop-B (residues 85-112) and loop-C (residues 178-192)</scene> which could play an important role in substrate entry. The residues of <scene name='80/806393/Cv/7'>the catalytic triad, Cys144, Glu81 and His169</scene>, are located at the N-terminus of helix α4, C-terminus of strand β5 and C-terminus of strand β11, respectively. | ||
| - | <scene name='80/806393/Cv/20'>Active-site of PCPdr with pG binding residues shown in ball-and-sticks and bound pG is shown in magenta ball-and-sticks</scene>. Water molecules are shown as red spheres. The presence of pG in the active site identifies the structural features that enable this enzyme to be a pG specific peptidase. pG is bound into a pocket formed by both hydrophobic and polar residues, Phe9, Phe12, Asn18, Val45, Gly70, Leu71, Tyr142, Val143, Cys144 and His169. The <scene name='80/806393/Cv/12'>residues of loop-A (residues 9-19)</scene> play a particularly important role in the pG binding. The <scene name='80/806393/Cv/13'>phenyl groups of Phe9 and Phe12 form stacking interactions with the aliphatic 2-pyrrolidone moiety of pG</scene> while the <scene name='80/806393/Cv/14'>ND2 of Asn18 forms a hydrogen bond with 2' oxygen of pyrrolidone moiety of pG</scene>. These residues are conserved in all the known PCPs I, including those from mammals. The residues from other loops also contribute significantly towards pG binding. The <scene name='80/806393/Cv/15'>main chain nitrogen and oxygen of Leu71 form two hydrogen bonds with OE and NH of pG</scene>, respectively. The adjacent residue, <scene name='80/806393/Cv/16'>Gly70</scene>, forms van der Waals contacts with OE of pG. Other van der Waals contacts for the pG binding are formed by the side chains of <scene name='80/806393/Cv/17'>Tyr142, Val143, Cys144 and Val45</scene>. The 5' carboxylate group of pG is held by several ionic interactions: <scene name='80/806393/Cv/18'>one of its carboxylate oxygen forms a hydrogen bond with NE2 of His169</scene> while the <scene name='80/806393/Cv/19'>other carboxylate oxygen interacts with the main chain N of catalytic Cys144 and a water molecule</scene>. This water molecule is further stabilized by its interactions with the residues Tyr142, Asn145, and Ala139. | + | <scene name='80/806393/Cv/20'>Active-site of PCPdr with pG binding residues shown in ball-and-sticks and bound pG is shown in magenta ball-and-sticks</scene>. Water molecules are shown as red spheres. The presence of pG in the active site identifies the structural features that enable this enzyme to be a pG specific peptidase. pG is bound into a pocket formed by both hydrophobic and polar residues, Phe9, Phe12, Asn18, Val45, Gly70, Leu71, Tyr142, Val143, Cys144 and His169. The <scene name='80/806393/Cv/12'>residues of loop-A (residues 9-19)</scene> play a particularly important role in the pG binding. The <scene name='80/806393/Cv/13'>phenyl groups of Phe9 and Phe12 form stacking interactions with the aliphatic 2-pyrrolidone moiety of pG</scene> while the <scene name='80/806393/Cv/14'>ND2 of Asn18 forms a hydrogen bond with 2' oxygen of pyrrolidone moiety of pG</scene>. These residues are conserved in all the known PCPs I, including those from mammals. The residues from other loops also contribute significantly towards pG binding. The <scene name='80/806393/Cv/15'>main chain nitrogen and oxygen of Leu71 form two hydrogen bonds with OE and NH of pG</scene>, respectively. The adjacent residue, <scene name='80/806393/Cv/16'>Gly70</scene>, forms van der Waals contacts with OE of pG. Other van der Waals contacts for the pG binding are formed by the side chains of <scene name='80/806393/Cv/17'>Tyr142, Val143, Cys144 and Val45</scene>. The 5' carboxylate group of pG is held by several ionic interactions: <scene name='80/806393/Cv/18'>one of its carboxylate oxygen forms a hydrogen bond with NE2 of His169</scene> while the <scene name='80/806393/Cv/19'>other carboxylate oxygen interacts with the main chain N of catalytic Cys144 and a water molecule</scene>. This water molecule is further stabilized by its interactions with the residues Tyr142, Asn145, and Ala139. <scene name='80/806393/Cv1/2'>Test</scene> |
<b>References</b><br> | <b>References</b><br> | ||
Revision as of 13:28, 24 January 2019
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