Structure of PDB 7mex Chain A

Receptor sequence

>7mexA (length=1737) Species: 559292 (Saccharomyces cerevisiae S288C)

GSLQGHIRRTLRSIHNLPYFRYTRGPTERADMSRALKEFIYRYLYFVISN
SGENLPTLFNAHPKQKLLTVFPDSLEDAVDIDKITSQQTIPFYKIDESRI
GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHV
CTDICTEFTSGICDCGDEEAWNSPLHCKAEEQEDVWNDSVNIALVELVLA
EVFDYFIDVFNQNIEPLPTIQKDITIKLREMTQQGKMYERAQFLNDLKYE
NDYMFDKIDPENYTVIIYNDEYHNYSQATTALRQGVPDNVHIDLLTSRID
GEGRAMLKCSQDLSSVLGGFFAVQTNGLSATLTSWSEYLHQETCKYIILW
ITHCLNIPNSSFQTTFRNMMGKTLCSEYLNATECRDMTPVVEKYFSNKFD
KNDPYRYIDLSILADGNQIPLGHHKILPESSTHSLSPLINDVETPTSRTY
SNTRLQHILYFDNRYWKRLRKDIQNVIIPTLASSNLYKPIFCQQVVEIFN
HITRSVAYMDREPQLTAIRECVVQLFTCPTNAKNIFENQSFLDIVWSIID
IFKEFCKVEGGVLIWQRVQKSNLTKSYSISFKQGLYTVETLLSKVHDPNI
PLRPKEIISLLTLCKLFNGAWKIKRKEGEHVLHEDQNFISYLEYTTSIYS
IIQTAEKVSEKSKDSIDSKLFLNAIRIISSFLGNRSLTYKLIYDSHEVIK
FSVSHERVAFMNPLQTMLSFLIEKVSLKDAYEALEDCSDFLKISDFSLRS
VVLCSQIDVGFWVRNGMSVLHQASYYKNNPELGSYSRDIHLNQLAILWER
DDIPRIIYNILDRWELLDWFTGEVDYQHTVYEDKISFIIQQFIAFIYQIL
TERQYFKTFSSLKDRRMDQIKNSIIYNLYMKPLSYSKLLRSVPDYLTEDT
TEFDEALEEVSVFVEPKGLADNGVFKLKASLYAKVDPLKLLNLENEFESS
ATIIKSHLAKDKDEIAKVVLIPQVSIKQLDKDALNLGAFTRNTVFAKVVY
KLLQVCLDMEDSTFLNELLHLVHGIFRDDELINGKDSIPEAYLSKPICNL
LLSIANAKSDVFSESIVRKADYLLEKMIMKKPNELFESLIASFGNQYVND
YKDKKLRTEKERKRRLAKKHQARLLAKFNNQQTKFMKEHESEFTCALCQD
SSSTDFFVIPAYHDHSPIFRPGNIFNPNEFMPMWDGFYNDDEKQAYIDDD
VLEALKENGSCGSRKVFVSCNHHIHHNCFKRYVQKKRFSSNAFICPLCQT
FSNCTLPLCQTSKANTGLSLDMFLESELSLDTLSRLFKPFTEENYRTINS
IFSLMISQCQGFDKAVRKRANFSHKDVSLILSVHWANTISMLEIASRLEK
PYSISFFRSREQKYKTLKNILVCIMLFTFVIGKPSMEFEPYPQQPDTVWN
QNQLFQYIVRSALFSPVSLRQTVTEALTTFSRQFLRDFLQGLSDAEQVTK
LYAKASKIGDVLKVSEQMLFALRTISDVRMEGLDSESIIYDLAYTFLLKS
LLPTIRRCLVFIKVLHELVKDSENETLVINGHEVEEELEFEDTAEFVNKA
LKMITEKESLVDLLTTQESIVSHPYLENIPYEYCGIIKLIDLSKYLNTYV
TQSKEIKLREERSQHMKNADNRLDFKICLTCGVKVHLRADRHEMTKHLNK
NCFKPFGAFLMPNSSEVCLHLTQPPSNIFISAPYLNSHGEVGRNAMRRGD
LTTLNLKRYEHLNRLWINNEIPGYISRVMGDEFRVTI

3D structure

• PDB: 7mex Structural insights into Ubr1-mediated N-degron polyubiquitination.
• Chain: A
• Resolution: 3.35 Å

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	A	L133 T144 T171 S172 G173 I174 D176 V571 T575	L121 T132 T159 S160 G161 I162 D164 V523 T527
BS02	ZN	A	C136 C139 H157 H160	C124 C127 H145 H148
BS03	ZN	A	C123 C151 C175	C111 C139 C163
BS04	ZN	A	H118 C151 C177 C189	H106 C139 C165 C177
BS05	ZN	A	C1703 H1722 C1727	C1628 H1647 C1652
BS06	ZN	A	C1295 H1297 C1320 C1323	C1220 H1222 C1245 C1248
BS07	ZN	A	C1220 H1300 C1303	C1145 H1225 C1228
BS08	ZN	A	H161 H1763 D1775	H149 H1688 D1700

Gene Ontology

Molecular Function

• GO:0004842 ubiquitin-protein transferase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding
• GO:0061630 ubiquitin protein ligase activity
• GO:1904855 proteasome regulatory particle binding

Biological Process

• GO:0000209 protein polyubiquitination
• GO:0006513 protein monoubiquitination
• GO:0016567 protein ubiquitination
• GO:0034620 cellular response to unfolded protein
• GO:0036503 ERAD pathway
• GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway
• GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
• GO:0072671 mitochondria-associated ubiquitin-dependent protein catabolic process
• GO:0090089 regulation of dipeptide transport
• GO:0120174 stress-induced homeostatically regulated protein degradation pathway
• GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0000151 ubiquitin ligase complex
• GO:0005737 cytoplasm
• GO:0008540 proteasome regulatory particle, base subcomplex
• GO:1990303 UBR1-RAD6 ubiquitin ligase complex

External links

• PDB: RCSB:7mex, PDBe:7mex, PDBj:7mex
• PDBsum: 7mex
• PubMed: 34789879
• UniProt: P19812|UBR1_YEAST E3 ubiquitin-protein ligase UBR1 (Gene Name=UBR1)