Sandbox Reserved 1477: Difference between revisions

Line 16:

Another glucose oxidase also tested with X-ray diffraction method in the same essay from '''Penicillium Amagasakiense''' has two identical chains in the PDB file which is the regular form of this type of enzyme. They have 81% sequence similarity and also very similar structures (which could be seen from the figure below).

Each chain of the enzyme contains a <scene name='80/800656/Fad/1'>FAD cofactor</scene> and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue <ref>PMID:10216293</ref>.

12 hydrogen bonds formed with the glucose (9 with residues, 2 with water molecules and 1 with the cofactor) as well as the hydrophobic effect of Phe-418 and Trp-430 stabilize the active site of the GOX <ref>PMID:10749686</ref>. As mentioned, the critical hydrogen bonds are the three hydrogen bonds formed between Arg-516 and 3-OH of the glucose based on the discussion of the function part.

[[Image: Different GOX.png]]

Fig. 1 Comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.

Each chain of the enzyme contains a <scene name='80/800656/Fad/1'>FAD cofactor</scene> and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue <ref>PMID:10216293</ref>.

[[Image:Position of FDA of GOX from PA.png]]

Fig. 2 Relative position of two FAD molecules of the penicillium amagasakiense (PDB code: 1gpe) with transparent surface, which will hopefully give a rough image about how the two chains of the enzyme are arranged. Since the 1cf3 file (GOX from aspergillus niger) only have one chain given, the 1gpe (GOX from penicillium amagasakiense) was used instead.

12 hydrogen bonds formed with the glucose (9 with residues, 2 with water molecules and 1 with the cofactor) as well as the hydrophobic effect of Phe-418 and Trp-430 stabilize the active site of the GOX <ref>PMID:10749686</ref>. As mentioned, the critical hydrogen bonds are the three hydrogen bonds formed between Arg-516 and 3-OH of the glucose based on the discussion of the function part.

[[Media:Movie compressed compressed.mp4]]

Sandbox Reserved 1477: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 16: / Line 16: @@
 Another glucose oxidase also tested with X-ray diffraction method in the same essay from '''Penicillium Amagasakiense''' has two identical chains in the PDB file which is the regular form of this type of enzyme. They have 81% sequence similarity and also very similar structures (which could be seen from the figure below).
+Each chain of the enzyme contains a <scene name='80/800656/Fad/1'>FAD cofactor</scene> and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue <ref>PMID:10216293</ref>.
+hydrogen bonds formed with the glucose (9 with residues, 2 with water molecules and 1 with the cofactor) as well as the hydrophobic effect of Phe-418 and Trp-430 stabilize the active site of the GOX <ref>PMID:10749686</ref>. As mentioned, the critical hydrogen bonds are the three hydrogen bonds formed between Arg-516 and 3-OH of the glucose based on the discussion of the function part.
 [[Image: Different GOX.png]]
 Fig. 1 Comparison between the structures of glucose oxidase from aspergillus niger (PDB code:1cf3, the tan part) and penicillium amagasakiense (PDB code: 1gpe, the cyan part). One of the chains of 1gpe was hidden.
-Each chain of the enzyme contains a <scene name='80/800656/Fad/1'>FAD cofactor</scene> and the molecules are tightly but non-covalently bonded to the enzyme <ref>PMID: 19374943</ref>. The residues of the active sites, Tyr-73, Phe-418, Trp-430, Arg-516, Asn-518, His-520 and His-563, locate around the cofactor. The cofactors locate at the interface between two chains of the enzyme, covered by an “irregular two-stranded antiparallel-sheet structure formed by residues 75-98”, which prevents the cofactors being released <ref>PMID:10216293</ref>. Generally speaking, the FAD molecules are tightly “covered” or “surrounded” by the enzyme. The binding sites with FAD of both enzymes (GOX’s from Aspergillus niger and Penicillium Amagasakiense) are almost identical with several exceptions of hydrogen-bonds-forming residues His-78 and Thr-110. These two residues are Gln-78 and Ser-100 in the GOX from Penicillium Amagasakiense. Flavin O4’s of the FAD cofactors in both enzymes are connected to the 110th residue (either Thr or Ser) and the Gly-108 residue <ref>PMID:10216293</ref>.
 [[Image:Position of FDA of GOX from PA.png]]
 Fig. 2 Relative position of two FAD molecules of the penicillium amagasakiense (PDB code: 1gpe) with transparent surface, which will hopefully give a rough image about how the two chains of the enzyme are arranged. Since the 1cf3 file (GOX from aspergillus niger) only have one chain given, the 1gpe (GOX from penicillium amagasakiense) was used instead.
-hydrogen bonds formed with the glucose (9 with residues, 2 with water molecules and 1 with the cofactor) as well as the hydrophobic effect of Phe-418 and Trp-430 stabilize the active site of the GOX <ref>PMID:10749686</ref>. As mentioned, the critical hydrogen bonds are the three hydrogen bonds formed between Arg-516 and 3-OH of the glucose based on the discussion of the function part.
 [[Media:Movie compressed compressed.mp4]]