Ubiquitin protein ligase

From Proteopedia

Revision as of 07:44, 11 July 2013

Template:STRUCTURE 1c4z

Ubiquitin-protein ligase (UPL) in combination with ubiquitin-conjugating enzyme (E2) causes the attachment of ubiquitin to lysine to a target protein. UPL can contain several distinct domains like: WW domains which contains 2 tryptophans which bind proline-rich peptide; UBA – Ubiquitin-Associated Domain; TKB – Tyrosine Kinase Binding domain; C2 – an 8 β strand domain which coordinates targeting proteins toward cell membrane; HECT – Homologous to the E6-AP Carboxyl Terminus; RING – Really Intersting New Gene involved in binding to E2; FHA – Forkhead Associated domain recognizing phosphothreonine; IBR – involved in binding to E2; PHD finger – Plant Homeo Domain is 50-80 amino acid long which contains a CHC motif; SRA – SET and RING-Associated domain; TUDOR – is a ca. 50 amino acids long and recognizes dimethylated arginine; CPH – protein-protein interaction domain; UBR – a ca. 70 amino acid long zinc finger-like domain; CUE – a ubiquitin-binding domain. For some details see

• TIR1 ubiquitin ligase
  
• Herbicide 2,4-D bound to TIR1 Ubiquitin Ligase.

3D Structures of ubiquitin protein ligase

Updated on 11-July-2013

UPL Cbl

2y1m – hUPL - human
1d5f – hUPL catalytic domain
2dk3 – hUPL catalytic domain - NMR
1yiu – hUPL WW3 domain - NMR
2oo9, 2ooa, 2oob – hUPL UBA domain
2do6, 2ekk, 2jnh, 2juj – hUPL UBA domain - NMR
3vgo – hUPL N terminal
2kr1 – hUPL N terminal - NMR
2ldr – hUPL helix-ring domain - NMR
2d9s – mUPL UBA domain – mouse - NMR

UPL Cbl complex

1yvh – hUPL TKB domain + APS adaptor protein
3bum, 3bun, 3buo, 3buw, 3bux, 3ob1, 3ob2, 3rlf, 3pfv – hUPL TKB domain + peptide
2y1n – hUPL residues 47-435 + ZAP peptide
4a4b, 4a4c – hUPL TKB domain (mutant) + ZAP peptide + ubiquitin conjugating enzyme E2
1c4z – hUPL catalytic domain + ubiquitin conjugating enzyme E2
4a49 – hUPL residues 354-435 + ubiquitin conjugating enzyme E2

UPL SIAH1

2a25 – hUPL substrate binding domain + calcyclin-binding protein peptide
2an6 – mUPL residues 92-282 + phyllopod peptide

UPL NEDD4

1wr3, 1wr4, 1wr7 – mUPL WW domain - NMR
2oni – hUPL catalytic domain
3b7y – hUPL C2 domain

UPL NEDD4 complex

1i5h – rUPL WW3 domain + amiloride-sensitive Na channel β subunit – rat
2ltx, 2lty – hUPL WW2 domain + peptide - NMR
2ez5 – UPL WW3 domain + COMM LPSY peptide – Drosophila melanogaster - NMR
2kpz, 2kq0, 2laj, 2ltz – hUPL WW3 domain + peptide - NMR
2lb2 – hUPL 2nd domain + peptide - NMR
3m7f – hUPL C2 domain + growth factor receptor bound protein
3jvz, 3jw0 – hUPL HECT domain + ubiquitin + ubiquitin-conjugating enzyme
2xbb – hUPL HECT domain + ubiquitin

UPL CNOT4

2cpi – mUPL RNA recognition motif - NMR

UPL RING2

2ckl – mUPL RING domain + polycomb group ring finger protein 4
2h0d – mUPL RING domain + B lymphoma MO-MLV insertion region
3h8h – hUPL C terminal
3gs2 – hUPL C terminal + chromobox protein homolog
3ixs – hUPL C terminal (mutant) + RING1 and YY1-binding protein

UPL RNF

2csw – hUPL FHA domain - NMR
3icu – hUPL protease-associated domain
3l11, 4ayc – hUPL RING domain
3v3l – hUPL WWE domain
2rsf – mUPL WWE domain + ATP
4epo – hUPL residues 345-485 + ubiquitin conjugating enzyme E2
4ap4 – hUPL residues 131-195 + ubiquitin conjugating enzyme E2 + ubiquitin

UPL PRKIN

2jmo – hUPL IBR domain - NMR
2pie – hUPL FHA domain
2zeq – hUPL ubiquitin-like domain
3b1l – mUPL ubiquitin-like domain
2knb – rUPL + endophilin - NMR

UPL ITCHY

2jo9 – mUPL WW3 domain + Epstein-Barr virus peptide - NMR
2joc, 2ysf, 2kyk – mUPL WW domain - NMR
3tug – hUPL HECT domain

UPL UHRF

3sox, 3zvz – hUPL PHD finger
2e6s, 2lgl – hUPL PHD finger - NMR
3bi7, 2pb7, 2zkg, 3dwh, 3oln – hUPL SRA domain
3db4 – hUPL TUDOR domain
3fl2 – hUPL RING domain

UPL UHRF complex

3clz, 2zkd, 2zke, 2zkf – hUPL SRA domain + DNA
2zo0, 2zo1, 2zo2, 3f8i, 3f8j, 3fde – mUPL SRA domain + DNA
3sou, 3sow, 3shb, 2lgg, 3t6r, zvy, 3ask, 3asl, 4gy5 – hUPL PHD finger + histone H3 peptide
2lgk – hUPL PHD finger + histone H3 peptide - NMR
3db3 – hUPL TUDOR domain + histone H3 peptide
[2l3r]] – hUPL TUDOR domain + histone H3 peptide - NMR

UPL SMURF

2jqz – hUPL - NMR
2kxq – hUPL WW2 and WW3 + peptide
2laz, 2lb0, 2lb1, 2ltx – hUPL WW + peptide - NMR
3pyc – hUPL C2 domain

UPL EDD1

2qho – hUPL UBA domain + ubiquitin

UPL LNX

3b76 – hUPL 3rd PDZ domain

UPL WWP1

2jqz – hUPL WW4 domain - NMR

UPL HECTD1

3dkm – hUPL CPH domain
[2lc3]] – hUPL helical bundle domain - NMR

UPL TRIM

3ddt – hUPL B2-box
3lrq – hUPL N terminal
3u5m – hUPL PHD+Bromo domains
3u5n, 3u5o, 3u5p – hUPL PHD+Bromo domain + H3-histone peptide

UPL HUWE1

3g1n – hUPL catalytic domain
3h1d – hUPL HECT domain (mutant)

UPL MYCBP2

3gbw – mUPL 1st PHR domain
3hwj – mUPL 2nd PHR domain

UPL HECW

3l4h – hUPL WW2 and helical box domains
2lfe – hUPL N terminal - NMR

UPL Arkadia

2kiz – hUPL RING-H2 finger domain - NMR

UPL UBR

3ny1, 3ny2 – hUPL UBR-box
3pt3 – hUPL C terminal
3ny3 – hUPL UBR-box + N-degron
3nih, 3nii, 3nij, 3nik, 3nil, 3nim, 3nin – yUPL UBR-box + peptide - yeast
3nis, 3nit – yUPL UBR-box
3ntw – rUPL MLLE domain + peptide

UPL Praja

2l0b – hUPL RING-type zinc finger domain - NMR

UPL CHFR

2xoc, 2xoy, 2xoz – hUPL C terminal + nucleotide
2xp0 – hUPL C terminal

UPL DTX3L

3pg6 – hUPL C terminal

UPL RSP5

3olm – hUPL HECT + WW3 domains + ubiquitin

UPL MYLIP

2yhn – hUPL RING domain
2yho – hUPL RING domain + ubiquitin-conjugating enzyme

UPL RBX

2lgv – hUPL residues 5-108 (mutant) - NMR
3rtr, 4f52 – hUPL residues 5-108 + cullin-1
4a0k – hUPL residues 12-108 + cullin-4B + cullin-associated NEDD8-dissociated protein
4a0l – hUPL residues 12-108 + cullin-4B + DNA damage-binding protein + DNA

UPL FANCL

3zqs – hUPL residues 109-294

UPL SOPA

3sy2 – UPL residues 165-782 + ubiquitin + ubiquitin-conjugating enzyme – Salmonella enterica

UPL HAKAI

3vk6 – mUPL phosphotyrosine-binding domain

UPL AMFR

4g3o – hUPL CUE domain
2lvn – hUPL CUE domain - NMR
2lvo, 2lvp, 2lvq – hUPL CUE domain + ubiquitin - NMR

UPL XIAP

4ic2 – hUPL RING domain
4ic3 – hUPL RING domain (mutant)
4hy0 – hUPL residues 238-357

UPL TIR1

2p1q – AtUPL + auxin response protein + SKP1-like protein – Arabidopsis thaliana
2p1q – AtUPL + auxin response protein + SKP1-like protein + herbicide

UPL MDM2

MDM2