User:Andrew Wills/Sandbox 1

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1diz, resolution 2.50Å ()

Ligands:

Non-Standard Residues:

Activity:

DNA-3-methyladenine glycosylase II, with EC number 3.2.2.21

Structural annotation:
Resources:	CATH : 1Diza02, 1Diza03, 1Diza01, 1Dizb01, 1Dizb02, 1Dizb03 InterPro : Ipr000035, Ipr003265, Ipr011257, Ipr010316, Ipr012294 Pfam : PF00730, PF06029 SCOP : d1diza1, d1diza2, d1dizb1, d1dizb2 UniProt : P04395

Functional annotation:
Biological process:	response to DNA damage stimulus base-excision repair DNA repair
Molecular function:	hydrolase activity DNA binding protein binding alkylbase DNA N-glycosylase activity

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

1 CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA
2 General Function
3 See Also
4 References

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

<nowiki>Insert non-formatted text here</nowiki>

General Function

1diz Escherichia coli 3 methyladenine DNA glycosylase II () is a DNA repair enzyme that initiates base excision repair for the removal of alkylated bases. There are many environmental toxins and cellular agents that may alkylate DNA bases. One example is Aflatoxin, a compound that is converted into a reactive epoxide by cytochrome P450 and attacks guanosine at its N-7 atom to form alkylated bases^[1]. The alkylated DNA bases prevent regulatory proteins from binding to DNA and blocks replicative polymerases.^[2] AlkA initiates base excision repair by first locating and binding to the alkylated DNA. It then flips the affected base out of the DNA double helix and into the active site of the enzyme. Once in the active site, AlkA hydrolyzes the glycosidic bond to release the damaged base and leave the sugar phosphate backbone intact. This creates the AP site that is either devoid of a purine or pyridine. The AP site signals to other base excision repair enzymes to insert an undamaged nucleotide based on the undamaged complementary strand and seal the DNA.

STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA (PDB entry 1diz)

Drag the structure with the mouse to rotate

Key Structures

AlkA is composed of three main domains with dimensions of approximately 50 Angstroms, 45 Angstroms, and 25 Angstroms.^[3] The first domain (residues 1-112) is the that is composed of a five stranded antiparallel beta sheet and two alpha helices.^[3] The (residues 113-230) contains seven alpha helices that create a hydrophobic core.^[3] The third domain (resudues 231-282) is the that contains a bundle of three alpha helices. ^[3] AlkA is a member of the helix-hairpin-helix (HhH) family of DNA glycosylases, where two compact alpha helical structures are connected by a hairpin loop.^[4] In AlkA, the is composed of residues 202-227 and is responsible for binding the damaged DNA by van der Waals interactions, a few hydrogen bonds, and metal ion interactions.

Active Sites and Mechanism

The HhH segment of AlkA connects to the phosphodiester backbone of DNA by hydrogen bonding and . The binding of the HhH segment to DNA stabilizes the damaged base and creates a 66 degree bend away from the protein that widens the minor groove of DNA.^[4] fits into the minor groove between base pairs and allows the alkylated base to be flipped into the active site.^[2] The AlkA active site is located where the second and third domains are separated by a deep nonpolar cleft that is lined with the aromatic side chains Phe18, Tyr273, Trp272, Tyr222, and Trp218.^[3] These side chains create a for the alkylated base.^[3] Once the damaged base is in the active site, stabilizes the flipped out alkylated base in the binding pocket by aromatic ring-stacking interactions.^[4] is essential for allowing the reaction to proceed, and points into the nonpolar pocket in order to allow stabilization of a carbocation intermediate. This stabilization is what allows the cleavage of the glycosidic bond on the damaged base.^[4] Mutation or inhibition of the Asp238 residue will prevent AlkA from performing base excision repair.

DNA Interaction

The AlkA protein stabilizes DNA by polar and nonpolar interactions with the DNA backbone. Molecular Level

Atomic Level

In order to keep the DNA strand bound to the protein, AlkA depends on van der Waals interactions on the minor groove of DNA. The van der Waals interactions play a major role in AlkA’s preference for double stranded DNA.^[2] An example of these interactions may be seen with the Pro175 wedged into the minor groove of DNA and anchoring it by van der Waals interctions.^[2]

References

↑ Berg, Jeremy, Tymoczko John, and Lubert Stryer. Biochemistry. 6th. New York: W.H. Freeman and Company, 2007. 806-808. Print.
↑ ^2.0 ^2.1 ^2.2 ^2.3 Hollis, Thomas, Yoshitaka Ichikawa, and Tom Ellenberger. "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO Journal. 19.4 (2000): 758-766. Print.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.
↑ ^4.0 ^4.1 ^4.2 ^4.3 Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print.

Proteopedia Page Contributors and Editors (what is this?)

Andrew B. Wills, Sayan Paria

Retrieved from "http://52.214.119.220/wiki/index.php/User:Andrew_Wills/Sandbox_1"

@@ Line 6: / Line 6: @@
 <nowiki><nowiki>Insert non-formatted text here</nowiki></nowiki>
 ==General Function==
-[[1diz]] Escherichia coli 3 methyladenine DNA glycosylase II (<scene name='56/566536/Alka_only/2'>AlkA</scene>) is a DNA repair enzyme that initiates base excision repair for the removal of alkylated bases. Aflatoxin B1 is an example of a toxin that attacks guanosine at its N-7 atom to form alkylated bases<ref name="Berg">Berg, Jeremy, Tymoczko John, and Lubert Stryer. Biochemistry. 6th. New York: W.H. Freeman and Company, 2007. 806-808. Print. </ref>, which prevent regulatory proteins from binding to DNA and blocks replicative polymerases.<ref name="Hollis">Hollis, Thomas, Yoshitaka Ichikawa, and Tom Ellenberger. "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO Journal. 19.4 (2000): 758-766. Print. </ref> AlkA initiates base excision repair by first locating and binding to the alkylated DNA. It then flips the affected base out of the DNA double helix and into the active site of the enzyme. Once in the active site, AlkA hydrolyzes the glycosidic bond to release the damaged base and leave the sugar phosphate backbone intact. This creates the AP site that is either devoid of a purine or pyridine. The AP site signals to other base excision repair enzymes to insert an undamaged nucleotide based on the undamaged complementary strand and seal the DNA.
+[[1diz]] Escherichia coli 3 methyladenine DNA glycosylase II (<scene name='56/566536/Alka_only/2'>AlkA</scene>) is a DNA repair enzyme that initiates base excision repair for the removal of alkylated bases. There are many environmental toxins and cellular agents that may alkylate DNA bases. One example is Aflatoxin, a compound that is converted into a reactive epoxide by cytochrome P450 and attacks guanosine at its N-7 atom to form alkylated bases<ref name="Berg">Berg, Jeremy, Tymoczko John, and Lubert Stryer. Biochemistry. 6th. New York: W.H. Freeman and Company, 2007. 806-808. Print. </ref>. The alkylated DNA bases prevent regulatory proteins from binding to DNA and blocks replicative polymerases.<ref name="Hollis">Hollis, Thomas, Yoshitaka Ichikawa, and Tom Ellenberger. "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO Journal. 19.4 (2000): 758-766. Print. </ref> AlkA initiates base excision repair by first locating and binding to the alkylated DNA. It then flips the affected base out of the DNA double helix and into the active site of the enzyme. Once in the active site, AlkA hydrolyzes the glycosidic bond to release the damaged base and leave the sugar phosphate backbone intact. This creates the AP site that is either devoid of a purine or pyridine. The AP site signals to other base excision repair enzymes to insert an undamaged nucleotide based on the undamaged complementary strand and seal the DNA.
 <StructureSection load='1diz' size='500' side='right' caption='STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA (PDB entry [[1diz]])' scene=''>

User:Andrew Wills/Sandbox 1

From Proteopedia

Revision as of 16:20, 6 November 2013

Contents

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

General Function

Key Structures

Active Sites and Mechanism

DNA Interaction

See Also

References

Proteopedia Page Contributors and Editors (what is this?)

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