Antizyme Inhibitor

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AzI crystallizes as a dimer such that the two monomers adopt a head-to-tail orientation similarly to the ODC dimer. The two AzI monomers demonstrate only <scene name='Antizyme_Inhibitor/Azi_odc1/1'>43 contacts</scene> (up 3.5 Å), while significantly more contacts are observed between the two monomers of hODC, mODC, and tODC (83, <scene name='Antizyme_Inhibitor/Azi_odc1/2'>74</scene>, and 69, respectively). Moreover, the surface area buried by the two AzI monomers is smaller than that buried by the mODC monomers. These properties support a very weak crystallographic dimer.
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The two AzI monomers (<font color='cyan'><b>cyan</b></font>, <font color='blueviolet'><b>blueviolet</b></font>) demonstrate only <scene name='Antizyme_Inhibitor/Azi_odc1/1'>43 contacts</scene> (up 3.5 Å), while there are more contacts between the two monomers of hODC, mODC <font color='red'><b>red</b></font>, <font color='lime'><b>lime</b></font>), and tODC (83, <scene name='Antizyme_Inhibitor/Azi_odc1/2'>74</scene>, and 69, respectively). Moreover, the surface area buried by the two mODC monomers is significantly larger than that buried by the AzI monomers. These features confirm a very weak crystallographic AzI dimer.
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Conserved hydrophobic residues in ODC form a zipper that stabilizes its homodimeric structure. These residues include F397(B), Y323(B), Y331(A), Y331(B), Y323(A), and F397(A) (the names of the chains are in brackets). An important residue Y331 in the <scene name='Antizyme_Inhibitor/Azi_odc1/3'>ODC zipper</scene> is substituted to S329 in AzI and interferes with the formation of a similar zipper in AzI. So, <scene name='Antizyme_Inhibitor/Azi_odc1/4'>mAzI</scene> showing the absence of the hydrophobic zipper. Many residues, that participate in the ODC interface interactions, are conserved among the ODCs from various species, but are different in AzI. Moreover, the residues that are conserved in AzI do not participate in interdimer interactions. These residues include the <scene name='Antizyme_Inhibitor/Azi_odc1/5'>two salt bridges</scene>, K169–D364 and D134–K294, which stabilize the ODC homodimer. In AzI, all these 4 residues (<scene name='Antizyme_Inhibitor/Azi_odc1/6'>K169-D362 and D134-K291</scene>, respectively) are conserved, but these two salt bridges are not formed. Two AzI monomers are positioned apart one from an other, in comparison ot ODC monomers, preventing the formation of interdimer interactions.
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The zipper, formed by conserved hydrophobic residues in mODC, stabilizes its dimeric structure. These residues involve F397(B), Y323(B), Y331(A), Y331(B), Y323(A), and F397(A) (the names of the chains are in brackets). Important in the <scene name='Antizyme_Inhibitor/Azi_odc1/3'>ODC zipper</scene> residue Y331 is substituted to S329 in AzI and interferes with the formation of a similar zipper in AzI. So, <scene name='Antizyme_Inhibitor/Azi_odc1/4'>mAzI</scene> showing the absence of the hydrophobic zipper. Many residues, that participate in the ODC interface interactions, are conserved among the ODCs from various species, but are different in AzI. Moreover, the residues that are conserved in AzI do not participate in interdimer interactions. These residues include the <scene name='Antizyme_Inhibitor/Azi_odc1/5'>two salt bridges</scene>, K169–D364 and D134–K294, which stabilize the ODC homodimer. In AzI, all these 4 residues (<scene name='Antizyme_Inhibitor/Azi_odc1/6'>K169-D362 and D134-K291</scene>, respectively) are conserved, but these two salt bridges are not formed. Two AzI monomers are positioned apart one from an other, in comparison ot ODC monomers, preventing the formation of interdimer interactions.
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Revision as of 14:56, 25 December 2008

Crystal structure of the Antizyme inhibitor

PDB ID 3BTN.pdb

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AzI, unpublished structure
Coordinates: save as pdb, mmCIF, xml



Publication Abstract from PubMed

Antizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine-induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 A resolution. Both AzI and ODC crystallize as a dimer. However, fewer interactions at the dimer interface, a smaller buried surface area, and lack of symmetry of the interactions between residues from the two monomers in the AzI structure suggest that this dimeric structure is nonphysiological. In addition, the absence of residues and interactions required for pyridoxal 5'-phosphate (PLP) binding suggests that AzI does not bind PLP. Biochemical studies confirmed the lack of PLP binding and revealed that AzI exists as a monomer in solution while ODC is dimeric. Our findings that AzI exists as a monomer and is unable to bind PLP provide two independent explanations for its lack of enzymatic activity and suggest the basis for its enhanced affinity toward Az.

Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function., Albeck S, Dym O, Unger T, Snapir Z, Bercovich Z, Kahana C, Protein Sci. 2008 May;17(5):793-802. Epub 2008 Mar 27. PMID:18369191

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.


PDB ID 3BTN.pdb

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Each consists of two domains: a α/β-barrel [1] domain (residues 45–280) and a modified [2] β-sheet domain (residues 8–44 and 281–435). Helices are colored in red and β strands in yellow.


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A sequence alignment and of mouse AzI crystallographic dimer (mAzI, cyan and blueviolet) to mouse, human, and trypanosome ODC (mODC (PDB code 7odc, red and lime), hODC, and tODC, respectively) show high sequence identity (~50%) and structural similarity between AzI and ODC monomers (RMSD values of 1.85 Å, 1.6 Å, and 1.5 Å, respectively). Superposition of the of mAzI and mODC showing the inter-subunit variable loops (AzI residues 355–362 and 387–401). AzI loops are in black, and ODC loops are in yellow.


The two AzI monomers (cyan, blueviolet) demonstrate only (up 3.5 Å), while there are more contacts between the two monomers of hODC, mODC red, lime), and tODC (83, , and 69, respectively). Moreover, the surface area buried by the two mODC monomers is significantly larger than that buried by the AzI monomers. These features confirm a very weak crystallographic AzI dimer. The zipper, formed by conserved hydrophobic residues in mODC, stabilizes its dimeric structure. These residues involve F397(B), Y323(B), Y331(A), Y331(B), Y323(A), and F397(A) (the names of the chains are in brackets). Important in the residue Y331 is substituted to S329 in AzI and interferes with the formation of a similar zipper in AzI. So, showing the absence of the hydrophobic zipper. Many residues, that participate in the ODC interface interactions, are conserved among the ODCs from various species, but are different in AzI. Moreover, the residues that are conserved in AzI do not participate in interdimer interactions. These residues include the , K169–D364 and D134–K294, which stabilize the ODC homodimer. In AzI, all these 4 residues (, respectively) are conserved, but these two salt bridges are not formed. Two AzI monomers are positioned apart one from an other, in comparison ot ODC monomers, preventing the formation of interdimer interactions.

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PLP-dependent enzymes have conserved active-site residues, implying that they have similar PLP binding sites. of the AzI and ODC structures suggests that AzI does not bind PLP. Many of the residues participated in PLP binding in ODC are not conserved in AzI. These include D88A, R154H, R277S, D332E, and Y389D (ODC residue numbering followed by the amino acid in AzI). Notably, the loss of even one of these interactions, as exemplified in the ODC R277A mutant, results in a 100-fold decrease in PLP binding as well as a 50% drop in Kcat and a 7-fold decrease in KM. PLP is in yellow, ODC residues D88, R154, R277, and Y389 are in green, and corresponding AzI residues A88, H154, S274, and D387 are in magenta.

Reference

Shira Albeck, Orly Dym, Tamar Unger, Zohar Snapir, Zippy Bercovich and Chaim Kahana. Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function. Protein Sci. 2008 May; 17(5): 793-802. Epub 2008 Mar 27.

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