The contribution of the hydrophobic contact in the C-capping motif of the alpha-helix to the thermodynamic stability of the ubiquitin molecule has been analyzed. For this, 16 variants of ubiquitin containing the full combinatorial set of four nonpolar residues Val, Ile, Leu, and Phe at C4 (Ile30) and C' ' (Ile36) positions were generated. The secondary structure content as estimated using far-UV circular dichroism (CD) spectroscopy of all but Phe variants at position 30 did not show notable changes upon substitutions. The thermodynamic stability of these ubiquitin variants was measured using differential scanning calorimetry, and it was shown that all variants have lower stability as measured by decreases in the Gibbs energy. Since in some cases the decrease in stability was so dramatic that it rendered an unfolded protein, it was therefore concluded that, despite apparent preservation of the secondary structure, the 30/36 hydrophobic contact is essential for the stability of the ubiquitin molecule. The decrease in the Gibbs energy in many cases was found to be accompanied by a large (up to 25%) decrease in the enthalpy of unfolding, particularly significant in the variants containing Ile to Leu substitutions. This decrease in enthalpy of unfolding is proposed to be primarily the result of the perturbed packing interactions in the native state of the Ile --> Leu variants. The analysis of these data and comparison with effects of similar amino acid substitutions on the stability of other model systems suggest that Ile --> Leu substitutions cannot be isoenergetic at the buried site. Study holds ProTherm entries: 8105, 8106, 8107, 8108, 8109, 8110, 8111, 8112, 8113, 8114, 8115, 8116, 8117, 8118, 8119, 8120, 8121, 8122, 8123, 8124, 8125, 8126, 8127, 8128, 8129, 8130, 8131, 8132, 8133, 8134, 8135, 8136, 8137, 8138, 8139, 8140, 8141, 8142, 8143, 8144, 8145, 8146, 8147, 8148, 8149, 8150, 8151, 8152, 8153, 8154, 8155, 8156, 8157, 8158, 8159, 8160, 8161, 8162, 8163, 8164, 8165, 8166, 8167, 8168, 8169, 8170, 8171, 8172, 8173, 8174, 8175, 8176, 8177, 8178, 8179, 8180, 8181, 8182, 8183, 8184, 8185, 8186, 8187, 8188, 8189, 8190, 8191, 8192, 8193, 8194, 8195, 8196, 8197, 8198, 8199, 14426, 14427, 14428, 14429, 14430, 14431, 14432, 14433, 14434, 14435, 14436, 14437, 14438 Extra Details: hydrophobic contact; nonpolar residues; secondary structure content;,packing interactions
ID: uBteUt3S4
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:35 p.m.
Version: 1
Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
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Structure ID | Release Date | Resolution | Structure Title |
---|---|---|---|
1BT0 | 1998-09-02T00:00:00+0000 | 1.7 | STRUCTURE OF UBIQUITIN-LIKE PROTEIN, RUB1 |
1OTR | 2003-03-22T00:00:00+0000 | 0 | Solution Structure of a CUE-Ubiquitin Complex |
7R81 | 2021-06-25T00:00:00+0000 | 2.7 | Structure of the translating Neurospora crassa ribosome arrested by cycloheximide |
3OLM | 2010-08-26T00:00:00+0000 | 2.5 | Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase |
4LCD | 2013-06-21T00:00:00+0000 | 3.1 | Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 |
5HPL | 2016-01-20T00:00:00+0000 | 2.31 | System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4 |
5TTE | 2016-11-03T00:00:00+0000 | 3.5 | Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic |
6NYA | 2019-02-11T00:00:00+0000 | 2.06 | Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin |
6NZO | 2019-02-14T00:00:00+0000 | 3.8 | Set2 bound to nucleosome |
6PX1 | 2019-07-24T00:00:00+0000 | 3.3 | Set2 bound to nucleosome |
Percent Identity | Matching Chains | Protein | Accession | Entry Name |
---|---|---|---|---|
100.0 | E3 ubiquitin-protein ligase RSP5 | P39940 | RSP5_YEAST | |
100.0 | A | Ubiquitin-binding protein CUE2 | P36075 | CUE2_YEAST |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CH06 | RL401_SCHPO |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CH07 | RL402_SCHPO |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CH08 | RL40A_YEAST |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CH09 | RL40B_YEAST |
100.0 | B | Ubiquitin-binding protein CUE2 | P40909 | RL40_CRYNJ |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CG73 | UBI1P_CANAX |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CG74 | UBI4P_CANAX |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CG75 | UBI4P_KLULA |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CG72 | UBI4P_SCHPO |
100.0 | B | Ubiquitin-binding protein CUE2 | P0CG63 | UBI4P_YEAST |
98.7 | B | Ubiquitin-binding protein CUE2 | P19848 | UBIQ_COPCO |
98.7 | B | Ubiquitin-binding protein CUE2 | P0C224 | RL40_NEUCR |
98.7 | B | Ubiquitin-binding protein CUE2 | P0CG70 | UBI4P_NEUCR |
97.4 | B | Ubiquitin-binding protein CUE2 | P59271 | R27AA_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | B9DHA6 | RL40A_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH34 | RL40A_ORYSJ |
97.4 | B | Ubiquitin-binding protein CUE2 | Q42202 | RL40B_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH35 | RL40B_ORYSJ |
97.4 | B | Ubiquitin-binding protein CUE2 | P51423 | RL40_BRARP |
97.4 | B | Ubiquitin-binding protein CUE2 | P49636 | RL40_NICSY |
97.4 | B | Ubiquitin-binding protein CUE2 | P62980 | RS27A_SOLLC |
97.4 | B | Ubiquitin-binding protein CUE2 | P62981 | RS27A_SOLTU |
97.4 | B | Ubiquitin-binding protein CUE2 | Q9SHE7 | RUB1_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | P0C073 | RUB1_DESAN |
97.4 | B | Ubiquitin-binding protein CUE2 | P0C030 | RUB1_ORYSJ |
97.4 | B | Ubiquitin-binding protein CUE2 | Q8RUC6 | RUB2_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | P0C031 | RUB2_ORYSJ |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CG85 | UBI1P_NICSY |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH04 | UBI1P_PETCR |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH05 | UBI2P_PETCR |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CG84 | UBI4P_NICSY |
97.4 | B | Ubiquitin-binding protein CUE2 | P69309 | UBIQP_AVEFA |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CG83 | UBIQP_HORVU |
97.4 | B | Ubiquitin-binding protein CUE2 | P69315 | UBIQP_LINUS |
97.4 | B | Ubiquitin-binding protein CUE2 | P69322 | UBIQP_PEA |
97.4 | B | Ubiquitin-binding protein CUE2 | P69325 | UBIQP_SOYBN |
97.4 | B | Ubiquitin-binding protein CUE2 | P69310 | UBIQ_AVESA |
97.4 | B | Ubiquitin-binding protein CUE2 | P69313 | UBIQ_HELAN |
97.4 | B | Ubiquitin-binding protein CUE2 | P69317 | UBIQ_LUPPO |
97.4 | B | Ubiquitin-binding protein CUE2 | P69326 | UBIQ_WHEAT |
97.4 | B | Ubiquitin-binding protein CUE2 | Q8H159 | UBQ10_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH33 | UBQ11_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | Q3E7T8 | UBQ14_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | Q1EC66 | UBQ3_ARATH |
97.4 | B | Ubiquitin-binding protein CUE2 | Q58G87 | UBQ3_ORYSJ |
97.4 | B | Ubiquitin-binding protein CUE2 | P0CH32 | UBQ4_ARATH |
100.0 | B | Ubiquitin-binding protein CUE2 | P69061 | RS27A_KLULA |
100.0 | B | Ubiquitin-binding protein CUE2 | P05759 | RS31_YEAST |
97.4 | B | Ubiquitin-binding protein CUE2 | P42740 | UBIQP_AGLNE |
96.1 | B | Ubiquitin-binding protein CUE2 | P42739 | UBIQP_ACEPE |
96.1 | B | Ubiquitin-binding protein CUE2 | Q3E7K8 | UBQ12_ARATH |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CH11 | RL401_CHLRE |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CH10 | RL403_CHLRE |
96.1 | B | Ubiquitin-binding protein CUE2 | P49632 | RL40_CAEEL |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG71 | UBIQ1_CAEEL |
96.1 | B | Ubiquitin-binding protein CUE2 | P59669 | UBIQP_GEOCY |
94.7 | B | Ubiquitin-binding protein CUE2 | Q9FHQ6 | UBQ9_ARATH |
96.1 | B | Ubiquitin-binding protein CUE2 | P49633 | RL40_ACACA |
98.7 | B | Ubiquitin-binding protein CUE2 | P14799 | RS27A_NEUCR |
96.1 | B | Ubiquitin-binding protein CUE2 | P63048 | RL40_BOVIN |
96.1 | B | Ubiquitin-binding protein CUE2 | P63050 | RL40_CANLF |
96.1 | B | Ubiquitin-binding protein CUE2 | P18101 | RL40_DROME |
96.1 | B | Ubiquitin-binding protein CUE2 | P63052 | RL40_FELCA |
96.1 | B | Ubiquitin-binding protein CUE2 | P62987 | RL40_HUMAN |
96.1 | B | Ubiquitin-binding protein CUE2 | P0C273 | RL40_MACFA |
96.1 | B | Ubiquitin-binding protein CUE2 | P62984 | RL40_MOUSE |
96.1 | B | Ubiquitin-binding protein CUE2 | P68205 | RL40_OPHHA |
96.1 | B | Ubiquitin-binding protein CUE2 | P63053 | RL40_PIG |
96.1 | B | Ubiquitin-binding protein CUE2 | P0C275 | RL40_PONPY |
96.1 | B | Ubiquitin-binding protein CUE2 | P62986 | RL40_RAT |
96.1 | B | Ubiquitin-binding protein CUE2 | P0C276 | RL40_SHEEP |
96.1 | B | Ubiquitin-binding protein CUE2 | P15357 | RS27A_DROME |
96.1 | B | Ubiquitin-binding protein CUE2 | P29504 | RS27A_MANSE |
96.1 | B | Ubiquitin-binding protein CUE2 | P68202 | RS27A_PLUXY |
96.1 | B | Ubiquitin-binding protein CUE2 | P68203 | RS27A_SPOFR |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG53 | UBB_BOVIN |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG54 | UBB_CAVPO |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG62 | UBB_CHICK |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG67 | UBB_GORGO |
96.1 | B | Ubiquitin-binding protein CUE2 | Q8MKD1 | UBB_HORSE |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG47 | UBB_HUMAN |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG49 | UBB_MOUSE |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG65 | UBB_PANTR |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG60 | UBB_PONPY |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG51 | UBB_RAT |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG55 | UBB_SHEEP |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CH28 | UBC_BOVIN |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG66 | UBC_GORGO |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG48 | UBC_HUMAN |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG50 | UBC_MOUSE |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG64 | UBC_PANTR |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG68 | UBC_PIG |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG61 | UBC_PONPY |
96.1 | B | Ubiquitin-binding protein CUE2 | Q63429 | UBC_RAT |
96.1 | B | Ubiquitin-binding protein CUE2 | P62976 | UBIQP_CRIGR |
96.1 | B | Ubiquitin-binding protein CUE2 | P0CG69 | UBIQP_DROME |
96.1 | B | Ubiquitin-binding protein CUE2 | P62972 | UBIQP_XENLA |
96.1 | B | Ubiquitin-binding protein CUE2 | Q865C5 | UBIQ_CAMDR |
96.1 | B | Ubiquitin-binding protein CUE2 | P68197 | UBIQ_CERCA |
96.1 | B | Ubiquitin-binding protein CUE2 | P62975 | UBIQ_RABIT |
94.7 | B | Ubiquitin-binding protein CUE2 | P33190 | RL40_TETPY |
94.7 | B | Ubiquitin-binding protein CUE2 | P0DJ25 | RL40_TETTS |
94.7 | B | Ubiquitin-binding protein CUE2 | P0C032 | RUB3_ORYSJ |
94.7 | B | Ubiquitin-binding protein CUE2 | P23324 | UBIQP_EUPEU |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG82 | UBIQP_TETPY |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CH27 | RL402_TRYCR |
94.7 | B | Ubiquitin-binding protein CUE2 | P46575 | RL40_EIMBO |
94.7 | B | Ubiquitin-binding protein CUE2 | P14795 | RL40_TRYCR |
94.7 | B | Ubiquitin-binding protein CUE2 | P14794 | RL40_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG76 | UBIQA_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG77 | UBIQD_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG78 | UBIQF_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG79 | UBIQG_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG81 | UBIQH_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG80 | UBIQI_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P0CG88 | UBIQJ_DICDI |
94.7 | B | Ubiquitin-binding protein CUE2 | P22589 | UBIQP_PHYIN |
94.7 | B | Ubiquitin-binding protein CUE2 | P23398 | UBIQP_STRPU |
94.7 | B | Ubiquitin-binding protein CUE2 | Q8SWD4 | UBIQ_ENCCU |
96.0 | B | Ubiquitin-binding protein CUE2 | P62992 | RS27A_BOVIN |
96.0 | B | Ubiquitin-binding protein CUE2 | P62978 | RS27A_CAVPO |
96.0 | B | Ubiquitin-binding protein CUE2 | P79781 | RS27A_CHICK |
96.0 | B | Ubiquitin-binding protein CUE2 | P62979 | RS27A_HUMAN |
96.0 | B | Ubiquitin-binding protein CUE2 | P68200 | RS27A_ICTPU |
96.0 | B | Ubiquitin-binding protein CUE2 | P62983 | RS27A_MOUSE |
96.0 | B | Ubiquitin-binding protein CUE2 | P62982 | RS27A_RAT |
93.4 | B | Ubiquitin-binding protein CUE2 | P69201 | RL40_LEIMA |
92.1 | B | Ubiquitin-binding protein CUE2 | P21899 | RL40_TRYBB |
100.0 | B | Ubiquitin-binding protein CUE2 | P0C016 | RS27A_SCHPO |
100.0 | B | Ubiquitin-binding protein CUE2 | P0C8R3 | RS27B_SCHPO |
97.2 | B | Ubiquitin-binding protein CUE2 | Q9ARZ9 | R27AA_ORYSJ |
97.2 | B | Ubiquitin-binding protein CUE2 | P59232 | R27AB_ARATH |
97.2 | B | Ubiquitin-binding protein CUE2 | P51431 | R27AB_ORYSJ |
97.2 | B | Ubiquitin-binding protein CUE2 | P59233 | R27AC_ARATH |
97.2 | B | Ubiquitin-binding protein CUE2 | P0CG86 | RS271_HORVU |
97.2 | B | Ubiquitin-binding protein CUE2 | P0CG87 | RS272_HORVU |
97.2 | B | Ubiquitin-binding protein CUE2 | P47905 | RS27A_LUPAL |
97.2 | B | Ubiquitin-binding protein CUE2 | P27923 | RS27A_MAIZE |
93.2 | B | Ubiquitin-binding protein CUE2 | P14797 | RS27A_DICDI |
90.8 | B | Ubiquitin-binding protein CUE2 | P69200 | RL40_LEITA |
97.1 | B | Ubiquitin-binding protein CUE2 | P59272 | RS27A_DAUCA |
90.8 | B | Ubiquitin-binding protein CUE2 | Q39256 | UBQ8_ARATH |
95.2 | B | Ubiquitin-binding protein CUE2 | P84589 | UBIQ_LUMTE |
97.5 | B | Ubiquitin-binding protein CUE2 | P31753 | RS27A_ASPOF |