Journal:Acta Cryst D:S2059798319000676
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<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/ | + | <scene name='80/806393/Cv1/11'>Structural conservation of loop-A in the crystal structures of PCPs from different prokaryotes</scene>. PCPdr (present study; gray); ''Thermus thermophlius'' (PDB entry [[2ebj]]; orange); ''Pyrococcus furiosus'' (PDB entry [[2df5]]; violet); ''Thermococcus litoralis'' (PDB entry [[1a2z]]; marine blue); ''Pyrococcus horikoshii'' (PDB entry [[1iu8]]; yellow); ''Bacillus amyloliquefaciens'' (PDB entry [[1aug]]; lime green); ''Bacillus anthrasis'' (PDB entry [[3lac]]; chocolate); ''Xenorhabdus bovienii'' (PDB entry [[4gxh]]; brown) and ''Staphylococcus aureus'' (PDB entry [[3giu]]; cyan). (Value in the bracket is reference of ''Bacillus amyloliquefaciens''). |
<b>References</b><br> | <b>References</b><br> | ||
Revision as of 11:20, 27 January 2019
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