Sandbox Reserved 1477: Difference between revisions

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Two PDB files mentioned in the essay, 1cf3 and 1gpe, which are two glucose oxidases from different organisms, ''aspergillus niger''' and '''Penicillium Amagasakiense'''. They have exactly the same types of ligands. The most important ligand is FAD cofactor, which assists the oxidation of beta-D-glucose. This essay was published back to 1999, which is fairly old in the scale of science.

== Structure ==

The structure of this PDB file (1cf3) contains only one chain with 4 different types of ligands. This is a 583-residue-long enzyme with a molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction.

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).

[[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 FAD cofactor 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 (Wohlfahrt, 1999).

[[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.

== Function ==

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== Structural highlights ==

~~<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />~~

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

The structure of this enzyme contains only one chain with 4 different types of ligands. This is a 583-residue-long protein with the molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction for the certain PDB entry with the code 1cf3. X-ray diffraction gives the information of the whole protein sequence (if the resolution of the instrument is high enough), which makes it better than any other methods with non-100% sequence courage.

Another glucose oxidase also tested with X-ray diffraction method in the same essay from Penicillium Amagasakiense has two identical chains. As mentioned, they have exactly the same ligands, which actually make sense since they have the same function.

[[Image:NAG and ASN.png]]

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@@ Line 12: / Line 12: @@
 Two PDB files mentioned in the essay, 1cf3 and 1gpe, which are two glucose oxidases from different organisms, ''aspergillus niger''' and '''Penicillium Amagasakiense'''. They have exactly the same types of ligands. The most important ligand is FAD cofactor, which assists the oxidation of beta-D-glucose. This essay was published back to 1999, which is fairly old in the scale of science.
+== Structure ==
+<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />
+The structure of this PDB file (1cf3) contains only one chain with 4 different types of ligands. This is a 583-residue-long enzyme with a molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction.
+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).
+[[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 FAD cofactor 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 (Wohlfahrt, 1999).
+[[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.
 == Function ==
@@ Line 20: / Line 35: @@
 == Structural highlights ==
-<Structure load='1cf3' size='350' frame='true' align='right' caption='The glucose oxidase from Aspergillus Niger (PDB#:1cf3)' scene='Insert optional scene name here' />
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
-The structure of this enzyme contains only one chain with 4 different types of ligands. This is a 583-residue-long protein with the molecular weight of about 65.8kDa. The structure is tested by X-ray diffraction for the certain PDB entry with the code 1cf3. X-ray diffraction gives the information of the whole protein sequence (if the resolution of the instrument is high enough), which makes it better than any other methods with non-100% sequence courage.
-Another glucose oxidase also tested with X-ray diffraction method in the same essay from Penicillium Amagasakiense has two identical chains. As mentioned, they have exactly the same ligands, which actually make sense since they have the same function.
 [[Image:NAG and ASN.png]]