The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
SUMO interaction site
Functional site description:
Non-covalent binding to SUMO proteins is mediated via the SUMO-interacting motif (SIM). SUMO-interacting proteins predominantly function in the nucleus. The SIM is essential for a variety of cellular processes including transcriptional regulation, sub-nuclear localization, nuclear body assembly, and anti-viral response. Viral proteins are also known to utilize such processes via their SIMs upon host cell invasion.
ELMs with same tags:
ELMs with same func. site: LIG_SUMO_SIM_anti_2  LIG_SUMO_SIM_par_1 
ELM Description:
This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the parallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 3rd position being more variable. At the variable 3rd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (2KQS, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.
Pattern: [DEST]{0,5}.[VILPTM][VIL][DESTVILMA][VIL].{0,1}[DEST]{1,10}
Pattern Probability: 0.0045452
Present in taxon: Eukaryota
Interaction Domain:
Rad60-SLD (PF11976) Ubiquitin-2 like Rad60 SUMO-like (Stochiometry: 1 : 1)
PDB Structure: 1Z5S
o See 33 Instances for LIG_SUMO_SIM_par_1
o Abstract
A SUMO-Interacting Motif or SIM (also known as SBM, for SUMO-Binding Motif) is a short linear motif that mediates non-covalent binding of SIM-containing proteins to SUMO. Known instances of SIM function in the nucleus. SIM-containing proteins are involved in cellular functions such as transcriptional regulation, subnuclear localization, nuclear body formation, DNA repair regulation, myeloid formation, tumor suppressor activation, control of differentiation/proliferation, targeting substrates for ubiquitin-mediated proteasomal degradation, and enhancement of sumoylation efficiency. It is of note that eukaryotic cells also utilize SIMs for anti-viral response (e.g. SIM is essential for PML’s (P29590) restriction activity of HSV-1 viral replication (Cuchet,2010)), whereas viruses in turn use SIM for transcriptional control of the host cell (e.g. SIM is essential for the trans-activation function of IE2 (Q6SWV3) protein of HCMV (Kim,2010)). Different SIM motif patterns have been suggested in the literature, but most of these match a limited number of known SIMs (Zhao,2014). The minimal region common to all known SIM instances and required for SIM function is a hydrophobic patch consisting of 3 to 4 hydrophobic residues (I, V, or L) with an optionally single variable residue at the 2nd or 3rd positions. At the variable position, beside hydrophobic residues, acidic- and phosphorylatable residues are alsoallowed. The hydrophobic core is extended at least on one side by a variable length stretch of residues composed of phosphorylatable residues (mainly Serine) and acidic residues. Acidic residues and phosphorylated Serine/Threonine residues increase the affinity of binding to SUMO due to interactions with basic residues of SUMO on the SIM interaction interface. Moreover, phosphorylation of the SIM provides a potential for regulation of sumoylation efficiency and fine-tuning the affinity of binding to SUMO, for instance S737 and S739 in Daxx (Q9UER7) (Chang,2011). Structural analyses of SIM complexed with SUMO have reported similar but slightly different binding patterns. All structurally solved instances of SIM bind as an extra beta strand in a hydrophobic pocket formed by the second beta strand and the single alpha helix of SUMO. The SIMs can bind in both directions to the hydrophobic pocket and therefore bind by either parallel or antiparallel beta-augmentation to the beta sheet of SUMO. RanBP2 (1Z5S) (Reverter,2005) and M-IR2 (2LAS) (Namanja,2012) bind in antiparallel orientation, PIAS2 (2ASQ) (Song,2005) and Daxx (2KQS) (Chang,2011) bind parallel to the second beta strand. The size of the interaction interface with SUMO differs slightly between SIMs. All known structures of SIMs commonly interact with the residues F36, K39, T42, K46, S50 and R54 of SUMO, while each SIM may additionally interact with other residues.
o 17 selected references:

o 9 GO-Terms:

o 33 Instances for LIG_SUMO_SIM_par_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P29590 PML
PML_HUMAN
555 566 EAEERVVVISSSEDSDAENS TP 4 Homo sapiens (Human)
2 
Q9Y6X2 PIAS3
PIAS3_HUMAN
446 451 SENKKKVEVIDLTIESSSDE TP 2 Homo sapiens (Human)
Q9UT72 rfp2
RFP2_SCHPO
37 42 GADVSEVTLLDLTRIPEFQP TP 4 Schizosaccharomyces pombe 972h-
Q9UT72 rfp2
RFP2_SCHPO
18 25 DQRLSPEVIDLTEDIEDDGA TP 4 Schizosaccharomyces pombe 972h-
Q9UKY1 ZHX1
ZHX1_HUMAN
536 549 DSSTTIIIDSSDETTESPTV TP 1 Homo sapiens (Human)
Q9UJ78 ZMYM5
ZMYM5_HUMAN
115 124 KGNISETIVIDDEEDIETNG TP 1 Homo sapiens (Human)
Q9UHP3 USP25
UBP25_HUMAN
90 95 VGSQADTNVIDLTGDDKDDL TP 2 Homo sapiens (Human)
Q9UER7 DAXX
DAXX_HUMAN
732 740 KTSVATQCDPEEIIVLSDSD TP 5 Homo sapiens (Human)
5 
Q9UBT2 UBA2
SAE2_HUMAN
586 598 EQDDVLIVDSDEEDSSNNAD TP 2 Homo sapiens (Human)
Q9NS56 TOPORS
TOPRS_HUMAN
906 915 ASRSPVVITIDSDSDKDSEV FP 2 Homo sapiens (Human)
Q99AM3 B-cell specific latent nuclear protein
Q99AM3_HHV8
475 481 SFASGLVIVSLRSGIYVKNL FP 2 Human herpesvirus 8
Q8N3Z6 ZCCHC7
ZCHC7_HUMAN
153 166 REVMIIEVSSSEEEESTISE TP 1 Homo sapiens (Human)
Q8N3Z6 ZCCHC7
ZCHC7_HUMAN
73 81 KPNQKKLIVLSDSEVIQLSD TP 1 Homo sapiens (Human)
Q8N2W9 PIAS4
PIAS4_HUMAN
464 469 ENGKPGADVVDLTLDSSSSS TP 3 Homo sapiens (Human)
Q7Z333 SETX
SETX_HUMAN
1012 1025 SRGQVIIISDSDDDDDERIL TP 2 Homo sapiens (Human)
Q6VMQ6 ATF7IP
MCAF1_HUMAN
965 970 ATGSDSSGVIDLTMDDEESG TP 2 Homo sapiens (Human)
Q6PEW1 ZCCHC12
ZCH12_HUMAN
276 282 LDDSDEDVILVESQDPPLPS TP 2 Homo sapiens (Human)
Q6PEW1 ZCCHC12
ZCH12_HUMAN
262 269 IGSADCNVIEIDDTLDDSDE TP 2 Homo sapiens (Human)
Q60793 Klf4
KLF4_MOUSE
99 104 RETEEFNDLLDLDFILSNSL TP 2 Mus musculus (House mouse)
Q13330 MTA1
MTA1_HUMAN
709 715 LPPRPPPPAPVNDEPIVIED TP 2 Homo sapiens (Human)
Q08562 ULS1
ULS1_YEAST
370 380 QKNSSIIILSDEDESGAGIN TP 1 Saccharomyces cerevisiae S288c
Q06265 EXOSC9
EXOS9_HUMAN
393 403 IILSDSEEEEMIILEPDKNP TP 1 Homo sapiens (Human)
P78317 RNF4
RNF4_HUMAN
45 50 LVETAGDEIVDLTCESLEPV TP 1 Homo sapiens (Human)
P78317 RNF4
RNF4_HUMAN
66 72 DLTHNDSVVIVDERRRPRRN TP 1 Homo sapiens (Human)
P78317 RNF4
RNF4_HUMAN
57 62 TCESLEPVVVDLTHNDSVVI TP 1 Homo sapiens (Human)
P49792 RANBP2
RBP2_HUMAN
2631 2637 DSPSDDDVLIVYELTPTAEQ TP 4 Homo sapiens (Human)
P40020 FIR1
FIR1_YEAST
758 767 DGKMVEVILLDEDEDVGLKN TP 1 Saccharomyces cerevisiae S288c
P39955 SAP1
SAP1_YEAST
231 237 YSDKYISEPILIDLTNDEDD TP 1 Saccharomyces cerevisiae S288c
P23497 SP100
SP100_HUMAN
322 332 NQASDIIVISSEDSEGSTDV TP 5 Homo sapiens (Human)
O75928 PIAS2
PIAS2_HUMAN
468 473 EASKKKVDVIDLTIESSSDE TP 6 Homo sapiens (Human)
2 
O75925 PIAS1
PIAS1_HUMAN
458 463 SNKNKKVEVIDLTIDSSSDE TP 2 Homo sapiens (Human)
3 
O13826 rfp1
RFP1_SCHPO
13 18 SNGIDESSVIDLTRSPSPPV TP 4 Schizosaccharomyces pombe 972h-
O00257 CBX4
CBX4_HUMAN
461 468 AALPQPEVILLDSDLDEPID TP 2 Homo sapiens (Human)
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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