PDBsum entry 9pap

Hydrolase (sulfhydryl proteinase)

PDB id: 9pap

Contents

Protein chain

212 a.a.

Ligands

MOH ×29

Waters ×195

References listed in PDB file

Key reference

Title

Structure of papain refined at 1.65 a resolution.

Authors

I.G.Kamphuis, K.H.Kalk, M.B.Swarte, J.Drenth.

Ref.

J Mol Biol, 1984, 179, 233-256. [DOI no: 10.1016/0022-2836(84)90467-4]

PubMed id

6502713

Abstract

Papain is a sulfhydryl protease from the latex of the papaya fruit. Its molecules consist of one polypeptide chain with 212 amino acid residues. The chain is folded into two domains with the active site in a groove between the domains. We have refined the crystal structure of papain, in which the sulfhydryl group was oxidized, by a restrained least-squares procedure at 1.65 A to an R-factor of 16.1%. The estimated accuracy in the atomic co-ordinates is 0.1 A, except for disordered atoms. All phi/psi angles for non-glycine residues are found within the outer limit boundary of a Ramachandran plot and this provides another check on the quality of the model. In the alpha-helical parts of the structure, the C = O bonds are directed more away from the helix axis than in a classical alpha-helix, leading to somewhat longer hydrogen bonds, 2.98 A, compared to 2.89 A. The hydrogen-bonding parameters and conformational angles in the anti-parallel beta-sheet structure show a large diversity. Hydrogen bonds in the core of the sheet are generally shorter than those at the more twisted ends. The average value is 2.91 A. The hydrogen bond distance Ni+3-Oi in turns is relatively long and the geometry is far from linear. Hydrogen bond formation, therefore, is perhaps not an essential prerequisite for turn formation. Although the crystallization medium is 62% (w/w) methanol in water, only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules. The water molecules play an important role in maintaining structural stability. This is specially true for internal water. Twenty-one water molecules are located in contact areas between adjacent papain molecules. It seems as if the enzyme is trapped in a grid of water molecules with only a limited number of direct interactions between the protein molecules. The residues in the active site cleft belong to the most static parts of the structure. In general, disorder in atomic positions increases when going from the interior of the protein molecule to its surface. This behavior was quantified and it was found that the point of minimum disorder is near the molecular centroid.

Figure 6.
FIG. 6. Schematic picture of the papain active site. Hydrogen bonds are shown as broken lines. M is a methanol and 42 a water molecule. A second water molecule is between Gln19 and Trp177.

The above figure is reprinted by permission from Elsevier: J Mol Biol (1984, 179, 233-256) copyright 1984.

Secondary reference #1

Title

Thiol proteases. Comparative studies based on the high-Resolution structures of papain and actinidin, And on amino acid sequence information for cathepsins b and h, And stem bromelain.

Authors

I.G.Kamphuis, J.Drenth, E.N.Baker.

Ref.

J Mol Biol, 1985, 182, 317-329. [DOI no: 10.1016/0022-2836(85)90348-1]

PubMed id

3889350

Figure 4.
Figure 4. The absolute values, IAx1( and (Ax2(, of the differences in side-chain conformational angles x1 and x2 for identical residues in papain and actinidin as a function of esidue number. The l-letter code is used to identify the amino acid residues.

Figure 6.
Figure 6. Similarity in solvent structure in actinidin nd papain crystals. The solvent molecules in actinidin re numbered in order of increasing B-value. The rdinate gives the number of identical sites for 20 consecutive water molecules in the actinidin crystal tructure. The hatched reas indicate the number of ethanol oxygen atoms in apain prsent on actinidin ater sites. he ptimal superposition matrix and vector were appled to the co-ordinates of the actinidin solvent olecules. Solvent sites were considered to b idential hen they were within a distance of 1.5 A.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Binding of chloromethyl ketone substrate analogues to crystalline papain.

Authors

J.Drenth, K.H.Kalk, H.M.Swen.

Ref.

Biochemistry, 1976, 15, 3731-3738. [DOI no: 10.1021/bi00662a014]

PubMed id

952885

Secondary reference #3

Title

The structure of papain.

Authors

J.Drenth, J.N.Jansonius, R.Koekoek, B.G.Wolthers.

Ref.

Adv Protein Chem, 1971, 25, 79.

PubMed id

4946704

Secondary reference #4

Title

Iv. Cysteine proteinases. The structure of the papain molecule.

Authors

J.Drenth, J.N.Jansonius, R.Koekoek, L.A.Sluyterman, B.G.Wolthers.

Ref.

Philos Trans R Soc Lond B Biol Sci, 1970, 257, 231-236.

PubMed id

4399047

Secondary reference #5

Title

Structure of papain.

Authors

J.Drenth, J.N.Jansonius, R.Koekoek, H.M.Swen, B.G.Wolthers.

Ref.

Nature, 1968, 218, 929-932.

PubMed id

5681232