Ubiquitin protein ligase

From Proteopedia

Revision as of 07:30, 17 December 2014

Template:STRUCTURE 1c4z

Ubiquitin-protein ligase (UPL) (E3) in combination with ubiquitin-conjugating enzyme (E2) causes the attachment of ubiquitin to lysine to a target protein. UPL XIAP or X-linked Inhibitor of Apoptosis Protein stops apoptosis induced by viral infection or by overproduction of caspases. UPL XIAP binds caspase-3, -7 and -9. UPL can contain several distinct domains like:

• WW domains which contain 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 C-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 – 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.
  

UPL XIAP consists of 3 BIR (baculoviral IAP repeat) domains, followed by UBA (ubiquitin-binding) domain and RING (C-terminal RING finger) domain. BIR2 inhibits caspase-3 and -7. BIR3 inhibits caspase-9. Overexpression of UPL XIAP functions as tumor marker. UPL XIAP is inhibited by Smac – a death signaling protein. For some details see

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

3D Structures of ubiquitin protein ligase

Updated on 17-December-2014 {{#tree:id=OrganizedByTopic|openlevels=0|

• Ubiquitin protein ligase AMFR

• • 4g3o – hUPL CUE domain
    
  • 2lvn – hUPL CUE domain - NMR
    
  • 2lxh – hUPL RING domain - NMR
    
  • 2lvo, 2lvp, 2lvq – hUPL CUE domain + ubiquitin - NMR
    
  • 2lxp – hUPL RING+G2BR domains + E2 G2 - NMR
    
  • 4lad – hUPL RING domain (mutant) + E2 G2
    

• Ubiquitin protein ligase Arkadia

• • 2kiz – hUPL RING-H2 finger domain - NMR
    

• Ubiquitin protein ligase CHFR

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

• Ubiquitin protein ligase Cbl

• • 2y1m – hUPL - human
    
  • 1d5f – hUPL catalytic domain
    
  • 2dk3 – hUPL catalytic domain - NMR
    
  • 1yiu – hUPL WW3 domain - NMR
    
  • 2k4d – hUPL RING domain
    
  • 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
    

• Ubiquitin protein ligase Cbl complex

• • 1yvh – hUPL TKB domain + APS adaptor protein
    
  • 3bum, 3bun, 3buo, 3buw, 3bux, 3ob1, 3ob2, 3rlf, 3pfv, 2k4d, 4gpl – 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
    

• Ubiquitin protein ligase CNOT4

• • 2cpi – mUPL RNA recognition motif - NMR
    

• Ubiquitin protein ligase DOA10

• • 2m6m – hUPL RING domain - NMR
    

• Ubiquitin protein ligase DTX3L

• • 3pg6 – hUPL C terminal
    

• Ubiquitin protein ligase E3

• • 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
    

• Ubiquitin protein ligase E3 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
    

• Ubiquitin protein ligase EDD1

• • 2qho – hUPL UBA domain + ubiquitin
    

• Ubiquitin protein ligase FANCL

• • 3zqs – hUPL residues 109-294
    
  • 4ccg – hUPL RING domain + E2 T
    

• Ubiquitin protein ligase HAKAI

• • 3vk6 – mUPL phosphotyrosine-binding domain
    

• Ubiquitin protein ligase HECTD1

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

• Ubiquitin protein ligase HECW

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

• Ubiquitin protein ligase HERC

• • 4o2w – hUPL 1 3rd RCC1-like domain
    
  • 4l1m – hUPL 2 1st RCC1-like domain
    

• Ubiquitin protein ligase HHARI

• • 4kbl, 4kc9 – hUPL
    
  • 2m9y – hUPL catalytic domain - NMR
    

• Ubiquitin protein ligase HUWE1

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

• Ubiquitin protein ligase ITCHY

• • 2jo9 – mUPL WW3 domain + Epstein-Barr virus peptide - NMR
    
  • 2joc, 2ysf, 2kyk – mUPL WW domain - NMR
    
  • 3tug – hUPL HECT domain
    
  • 2nq3 – hUPL C2 domain
    
  • 2dmv – mUPL WW2 domain - NMR
    

• Ubiquitin protein ligase LNX

• • 3vqf – mUPL 2rd PDZ domain
    
  • 3b76 – hUPL 3rd PDZ domain
    
  • 3vqg – mUPL 2rd PDZ domain + peptide
    

• Ubiquitin protein ligase MDM2 see MDM2

• Ubiquitin protein ligase MYCBP2

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

• Ubiquitin protein ligase MYLIP

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

• Ubiquitin protein ligase NEDD4

• • 1wr3, 1wr4, 1wr7 – mUPL WW domain - NMR
    
  • 2oni – hUPL catalytic domain
    
  • 3b7y – hUPL C2 domain
    
  • 2xbf – hUPL HECT domain
    
  • 4be8 – hUPL HECT domain (mutant)
    

• Ubiquitin protein ligase 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, 2m3o – hUPL WW3 domain + peptide - NMR
    
  • 4n7h – hUPL WW3 domain + arrestin peptide
    
  • 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
    
  • 4bbn – hUPL HECT domain (mutant) + polyubiquitin
    

• Ubiquitin protein ligase Praja

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

• Ubiquitin protein ligase PARKIN

• • 4k95 – rUPL
    
  • 2jmo – hUPL IBR domain - NMR
    
  • 2zeq – hUPL ubiquitin-like domain
    
  • 4bm9, 4i1h – hUPL catalytic domain
    
  • 4i1f – hUPL catalytic domain (mutant)
    
  • 3b1l – mUPL ubiquitin-like domain
    
  • 4k7d – rUPL C terminal domain
    
  • 2knb – rUPL + endophilin - NMR
    

• Ubiquitin protein ligase RAD18

• • 2y43 – hUPL RING domain
    

• Ubiquitin protein ligase RBBP6

• • 3ztg – hUPL RING domain - NMR
    

• Ubiquitin protein ligase RBX

• • 2lgv – hUPL residues 5-108 (mutant) - NMR
    
  • 3rtr, 4f52 – hUPL residues 5-108 + cullin-1
    
  • 4a0k, 4a0c – hUPL residues 12-108 + cullin-4B + cullin-associated NEDD8-dissociated protein
    
  • 4a0l – hUPL residues 12-108 + cullin-4B + DNA damage-binding protein + DNA
    

• Ubiquitin protein ligase 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
    
  • 3rpg – hUPL + polycomb complex protein BMI-1 + E2 D3
    

• Ubiquitin protein ligase RNF

• • 4ppe – hUPL RING domain
    
  • 4ap4 – hUPL 4 residues 131-195 + E2 + ubiquitin
    
  • 2pie – hUPL 8 FHA domain
    
  • 2csw – hUPL 8 FHA domain - NMR
    
  • 4ayc, 4gb0 – hUPL 8 RING domain
    
  • 4epo, 4orh – hUPL 8 residues 345-485 + E2
    
  • 4juy, 4oyj, 4p09 – hUPL 31 PUB domain
    
  • 4ljq – hUPL 31 catalytic domain
    
  • 4ljo – hUPL 31 catalytic domain + ubiquitin
    
  • 4ljp – hUPL 31 catalytic domain (mutant) + ubiquitin
    
  • 4owf – hUPL 31 catalytic domain + nf-κ-B modulator
    
  • 4oyk, 4p0b – hUPL 31 PUB domain + otulin
    
  • 4p0a – hUPL 31 PUB domain + p97 peptide
    
  • 4kng – hUPL 43 PA domain + LGR5 + RSPO1
    
  • 2ma6 – hUPL 123 RING domain - NMR
    
  • 3icu – hUPL 128 protease-associated domain
    
  • 3v3l – hUPL 146 WWE domain
    
  • 2rsf – mUPL 146 WWE domain + ATP
    
  • 3l11, 4gb0 – hUPL 168 RING domain
    

• Ubiquitin protein ligase RSP

• • 4lcd – hUPL 3 HECT + WW3 domains (mutant) + SNA3 peptide + ubiquitin
    
  • 3olm – hUPL 5 HECT + WW3 domains + ubiquitin
    

• Ubiquitin protein ligase SHPRH

• • 2m85 – hUPL PHD domain - NMR
    

• Ubiquitin protein ligase SIAH1

• • 4c9z, 4ca1 – hUPL zinc finger+substrate binding domains
    
  • 2a25 – hUPL substrate binding domain + calcyclin-binding protein peptide
    
  • 4i7b, 4i7d – hUPL C terminal + phyllopod peptide
    
  • 4i7c – hUPL C terminal (mutant) + phyllopod peptide
    
  • 2an6 – mUPL residues 92-282 + phyllopod peptide
    

• Ubiquitin protein ligase SMURF

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

• Ubiquitin protein ligase SOPA

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

• Ubiquitin protein ligase SSPH1

• • 4nkh –SeUPL 21 LRR domain
    
  • 4nkg –SeUPL 21 LRR domain + Ser/Thr protein kinase N1 peptide
    

• Ubiquitin protein ligase TIR1

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

• Ubiquitin protein ligase TRIM

3zo0 – mUPL 21 residues 291-470 + IG γ-2A
4b8e – mUPL 25 PRY-SPRY domain
3u5m – hUPL 33 PHD+Bromo domains
3u5n, 3u5o, 3u5p – hUPL 33 PHD+Bromo domain + H3-histone peptide
3ddt – hUPL 37 B2-box
4m3l – hUPL 63 coiled-coil domain
4nqj – hUPL 69 coiled-coil domain

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 UHRF (Np95)

3sox, 3zvz – hUPL 1 PHD finger
2lgl – hUPL 1 PHD finger - NMR
2e6s – hUPL 2 PHD finger - NMR
3zvy – hUPL 1 PHD finger + histone H3 peptide
3bi7, 2pb7, 2zkg, 3dwh – hUPL 1 SRA domain
3oln – hUPL 2 SRA domain
3db4 – hUPL 1 TUDOR domain
3fl2 – hUPL 1 RING domain

UPL UHRF complex

3clz, 2zkd, 2zke, 2zkf – hUPL 1 SRA domain + DNA
4pw5, 4pw6, 4pw7 – hUPL 2 SRA domain + DNA
2zo0, 2zo1, 2zo2, 3f8i, 3f8j, 3fde – mUPL 1 SRA domain + DNA
3sou, 3sow, 3shb, 2lgg, 3t6r, 3ask, 3asl, 4gy5 – hUPL 1 PHD finger + histone H3 peptide
2lgk – hUPL 1 PHD finger + histone H3 peptide - NMR
3db3 – hUPL 1 TUDOR domain + histone H3 peptide
2l3r – hUPL 1 TUDOR domain + histone H3 peptide - NMR

UPL WWP1

2jqz – hUPL WW4 domain - NMR

UPL XIAP

XIAP BIR-1 domain

2poi, 2qra – hXIAP – human
2pop – hXIAP + TAB1

XIAP BIR-2 domain

1c9q – hXIAP (mutant) – NMR
4j3y – hXIAP (mutant)
4j44, 4j45, 4j46, 4j47, 4j48 - hXIAP (mutant) + peptide
1i3o – hXIAP (mutant) + caspase-3
1i4o, 1kmc, 1i51 – hXIAP + caspase-7
4kmp - hXIAP + inhibitor
4kju, 4kjv - hXIAP (mutant) + inhibitor
3uw5 – hXIAP residues 63-179 (mutant) + GDC0152 + inhibitor

XIAP BIR-3 domain

1f9x – hXIAP – NMR
1g3f – hXIAP + Smac peptide – NMR
2opz – hXIAP + Smac peptide
2opy, 2vsl, 3clx, 3cm2, 3cm7, 2jk7, 3eyl, 3g76, 4ec4 – hXIAP + Smac mimic
1g73 – hXIAP + Smac
1nw9 – hXIAP + caspase-9
1tfq, 1tft – hXIAP + inhibitor - NMR
3hl5, 4hy0 – hXIAP + inhibitor
3uw4 – hXIAP (mutant) + peptide + inhibitor

XIAP UBA domain

2kna – hXIAP – NMR

XIAP RING domain

4ic2 – hXIAP
2ecg – hXIAP – NMR
4ic3 – hXIAP (mutant)

UPL ZNRF3

4c84, 4c85, 4c86, 4c8a, 4c8c, 4c8f – zUPL ectodomain – zebra fish
4c8p – zUPL ectodomain (mutant)
4c8t, 4c8u – fUPL ectodomain – frog
4cdj – mUPL ectodomain
4c99, 4c9a, 4c9e, 4c9r, 4c9u, 4cdk – mUPL ectodomain + R-spondin

UPL ZFP91

2m9a – hUPL residues 370-456 - NMR