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PDBsum entry 1gge

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Oxidoreductase PDB id
1gge
Jmol
Contents
Protein chains
727 a.a. *
Ligands
HDD ×4
Waters ×3208
* Residue conservation analysis

References listed in PDB file
Key reference
Title Substrate flow in catalases deduced from the crystal structures of active site variants of hpii from escherichia coli.
Authors W.Melik-Adamyan, J.Bravo, X.Carpena, J.Switala, M.J.Maté, I.Fita, P.C.Loewen.
Ref. Proteins, 2001, 44, 270-281. [DOI no: 10.1002/prot.1092]
PubMed id 11455600
Abstract
The active site of heme catalases is buried deep inside a structurally highly conserved homotetramer. Channels leading to the active site have been identified as potential routes for substrate flow and product release, although evidence in support of this model is limited. To investigate further the role of protein structure and molecular channels in catalysis, the crystal structures of four active site variants of catalase HPII from Escherichia coli (His128Ala, His128Asn, Asn201Ala, and Asn201His) have been determined at approximately 2.0-A resolution. The solvent organization shows major rearrangements with respect to native HPII, not only in the vicinity of the replaced residues but also in the main molecular channel leading to the heme distal pocket. In the two inactive His128 variants, continuous chains of hydrogen bonded water molecules extend from the molecular surface to the heme distal pocket filling the main channel. The differences in continuity of solvent molecules between the native and variant structures illustrate how sensitive the solvent matrix is to subtle changes in structure. It is hypothesized that the slightly larger H(2)O(2) passing through the channel of the native enzyme will promote the formation of a continuous chain of solvent and peroxide. The structure of the His128Asn variant complexed with hydrogen peroxide has also been determined at 2.3-A resolution, revealing the existence of hydrogen peroxide binding sites both in the heme distal pocket and in the main channel. Unexpectedly, the largest changes in protein structure resulting from peroxide binding are clustered on the heme proximal side and mainly involve residues in only two subunits, leading to a departure from the 222-point group symmetry of the native enzyme. An active role for channels in the selective flow of substrates through the catalase molecule is proposed as an integral feature of the catalytic mechanism. The Asn201His variant of HPII was found to contain unoxidized heme b in combination with the proximal side His-Tyr bond suggesting that the mechanistic pathways of the two reactions can be uncoupled.
Figure 1.
Figure 1. Stereo views of the heme environment. A: Native HPII. B: His128Ala variant. C: Asn201His variant. For clarity, only the catalytically important residues His128, Ser167, and Asn201 on the heme distal side and His392, Arg411, and Tyr415 on the heme proximal side are explicitly shown. Also displayed are the conserved residues lining the channel, Val169, Asp181, Phe207, and Phe217. The ring of hydrophobic residues that include Val169 define the narrowest point in the major channel. Heme d is evident only in native HPII (A), and the covalent bond between the side-chains of His392 and Tyr415 is evident in native HPII (A) and the Asn201His variant (C). Changes in solvent organization are evident among the three structures. Water molecules in the native enzyme, and their equivalent in the variants, are labeled numerically, W1-W8. Water molecules in the variant structures with no correspondence in native HPII are labeled alphabetically, WA-WE. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.].
Figure 2.
Figure 2. Stereo views showing the opening of the major channel into the heme distal side pocket in the His128Ala variant structure. A: Averaged omit (F[o] - F[c]) electron-density map shown with a chicken wire representation. Density corresponding to the chain of omitted water molecules is clearly defined filling the heme distal side pocket and the major channel. B: The accessible surface, calculated with the program VOIDOO, emphasizes the continuity of the channel and of the chain of solvent molecules found inside. Red spheres, water molecules; dashed lines, hydrogen bonds among water molecules in the channel; dotted lines, iron coordination.
The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 44, 270-281) copyright 2001.
Secondary reference #1
Title Crystal structure of catalase hpii from escherichia coli.
Authors J.Bravo, N.Verdaguer, J.Tormo, C.Betzel, J.Switala, P.C.Loewen, I.Fita.
Ref. Structure, 1995, 3, 491-502. [DOI no: 10.1016/S0969-2126(01)00182-4]
PubMed id 7663946
Full text Abstract
Figure 2.
Figure 2. Representative stereoviews of the final averaged (2F[o]–F[c]) electron-density map. Residues (a) Ile274 and (b) His739 are outside energetically favorable regions in the Ramachandran diagram (see Figure 3). The identification of the bulky residue Trp742 (b) facilitated the tracing of the C-terminal domain. (c) Exposed segment in the hinge region, including residues Pro575-Pro576-Pro577. Figure 2. Representative stereoviews of the final averaged (2F[o]–F[c]) electron-density map. Residues (a) Ile274 and (b) His739 are outside energetically favorable regions in the Ramachandran diagram (see [5]Figure 3). The identification of the bulky residue Trp742 (b) facilitated the tracing of the C-terminal domain. (c) Exposed segment in the hinge region, including residues Pro575-Pro576-Pro577.
Figure 10.
Figure 10. Stereoview of the electron density in the terminal carboxylate environment (residue Ala753). The molecular dyad R-axis-related residues are shown with thinner bonds. The terminal carboxylate charged group appears to be neutralized by Lys309. Figure 10. Stereoview of the electron density in the terminal carboxylate environment (residue Ala753). The molecular dyad R-axis-related residues are shown with thinner bonds. The terminal carboxylate charged group appears to be neutralized by Lys309.
The above figures are reproduced from the cited reference with permission from Cell Press
Secondary reference #2
Title Structure of the heme d of penicillium vitale and escherichia coli catalases.
Authors G.N.Murshudov, A.I.Grebenko, V.Barynin, Z.Dauter, K.S.Wilson, B.K.Vainshtein, W.Melik-Adamyan, J.Bravo, J.M.Ferrán, J.C.Ferrer, J.Switala, P.C.Loewen, I.Fita.
Ref. J Biol Chem, 1996, 271, 8863-8868.
PubMed id 8621527
Abstract
Secondary reference #3
Title Structure of catalase hpii from escherichia coli at 1.9 a resolution.
Authors J.Bravo, M.J.Mate, T.Schneider, J.Switala, K.Wilson, P.C.Loewen, I.Fita.
Ref. Proteins, 1999, 34, 155-166. [DOI no: 10.1002/(SICI)1097-0134(19990201)34:2<155::AID-PROT1>3.0.CO;2-P]
PubMed id 10022351
Full text Abstract
Figure 5.
Figure 5. Structure of the C-terminal domain of HPII including interactions between this domain and the core of the same subunit. The lower panel shows a stereo view of the C-terminal domain. The residues involved in the 12 interactions between the domain and the core (Table II) are also shown. The side panel displays most of the solvent molecules that fill the interface between the C-terminal domain and the core of HPII. The corresponding (2F[o] - F[c]) electron density map is also shown. The location of the two regions within the tetramer are indicated in boxes in the upper panel.
Figure 9.
Figure 9. Diagrammatic representation showing the key elements in the heme environment of HPII. The essential or important residues, His128, Ser167, Asn201, Thr203, His392, and Tyr415 are indicated. Solvent molecules bound to these residues are also shown. The water molecule closest to the iron appears to exhibit high mobility, probably with two main dispositions, compatible with a weak coordination. The heme component is cis-hydroxychlorin -spirolactone in an orientation that is flipped 180^o with respect to the orientation of the heme in BLC.
The above figures are reproduced from the cited reference with permission from John Wiley & Sons, Inc.
PROCHECK
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