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(-) Description

Title :  STRUCTURE OF A20 OTU DOMAIN BOUND TO UBIQUITIN
 
Authors :  T. E. T. Mevissen, Y. Kulathu, M. P. C. Mulder, P. P. Geurink, S. L. Maslen M. Gersch, P. R. Elliott, J. E. Burke, B. D. M. Van Tol, M. Akutsu, F. El M. Kawasaki, S. M. V. Freund, H. Ovaa, D. Komander
Date :  22 Aug 16  (Deposition) - 19 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  F  (1x)
Keywords :  Hydrolase, Protease, Deubiquitinase, Otu Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Mevissen, Y. Kulathu, M. P. Mulder, P. P. Geurink, S. L. Maslen, M. Gersch, P. R. Elliott, J. E. Burke, B. D. Van Tol, M. Akutsu, F. El Oualid, M. Kawasaki, S. M. Freund, H. Ovaa, D. Komander
Molecular Basis Of Lys11-Polyubiquitin Specificity In The Deubiquitinase Cezanne.
Nature V. 538 402 2016
PubMed-ID: 27732584  |  Reference-DOI: 10.1038/NATURE19836

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3
    Chains: A, C
    EC Number: 3.4.19.12, 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TNFAIP3, OTUD7C
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TNF ALPHA-INDUCED PROTEIN 3,OTU DOMAIN-CONTAINING PROTEIN 7C,PUTATIVE DNA-BINDING PROTEIN A20,ZINC FINGER PROTEIN A20
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLY76 WAS REPLACED WITH PROPARGYLAMIDE
 
Molecule 3 - TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3
    Chains: E, F
    EC Number: 3.4.19.12, 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TNFAIP3, OTUD7C
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CYS103 IS OXIDIZED
    Synonym: TNF ALPHA-INDUCED PROTEIN 3,OTU DOMAIN-CONTAINING PROTEIN 7C,PUTATIVE DNA-BINDING PROTEIN A20,ZINC FINGER PROTEIN A20

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     E 
Biological Unit 4 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AYE2Mod. Amino AcidPROP-2-EN-1-AMINE
2CSD2Mod. Amino Acid3-SULFINOALANINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AYE1Mod. Amino AcidPROP-2-EN-1-AMINE
2CSD-1Mod. Amino Acid3-SULFINOALANINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AYE1Mod. Amino AcidPROP-2-EN-1-AMINE
2CSD-1Mod. Amino Acid3-SULFINOALANINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1AYE-1Mod. Amino AcidPROP-2-EN-1-AMINE
2CSD1Mod. Amino Acid3-SULFINOALANINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1AYE-1Mod. Amino AcidPROP-2-EN-1-AMINE
2CSD1Mod. Amino Acid3-SULFINOALANINE

(-) Sites  (0, 0)

(no "Site" information available for 5LRX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LRX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LRX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LRX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LRX)

(-) Exons   (0, 0)

(no "Exon" information available for 5LRX)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..eeeee..eee......eeee....eee.....hhhhh....eeeeee..eeeeeee.........eee.eee....eee......hhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lrx A   4 QVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTPLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQE 358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      |188       198       208       218       228       238       248       258       268       278       288       298       308       320       330       340       350        
                                                                                                                                                                                                          180|                                                                                                                                317|                                      
                                                                                                                                                                                                           186                                                                                                                                 320                                      


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5lrx B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGx  76
                                    10        20        30        40        50        60        70     |
                                                                                                      76-AYE


Chain C from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhh............hhhhhhhhhhhh...eeeee..ee.........ee....eee.....hhhhh....eeeeee..eeeeeee.........eee.eeee..eeee......hhhhhhhhhhhhhhhh.eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lrx C   4 QVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTPGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQEN 359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      |187       197       207       217       227       237       247       257       267       277       287       297       307       323       333       343       353      
                                                                                                                                                                                                          180|                                                                                                                               315|                                     
                                                                                                                                                                                                           185                                                                                                                                322                                     


Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5lrx D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGx  76
                                    10        20        30        40        50        60        70     |
                                                                                                      76-AYE


Chain E from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.hhh.ee........ee.hhhhh..ee......hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhh..eeee...eee.......eee....eee.....hhhhh....eeeeee..eeeeeeee........eee.eeee..eeee......hhhhhhhhhhhhhhhh.eeeeeee.hhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lrx E   4 QVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQNWNDEWDNLIKMASTDTPQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQEN 359
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      |165       175    || 191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351        
                                                                                                                             103-CSD                                        150|              180|                                                                                                                                                                            
                                                                                                                                                                             163               187                                                                                                                                                                            


Chain F from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..ee......hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhh..eeee...eee...eee....eee.....hhhhh....eeeee....eeeeeee........eee.eeee..eeee......hhhhhhhhhhhhhhhh.eeeeeee.hhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lrx F   4 QVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSNDEWDNLIKMASTDTPLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKW 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     ||168       178 ||    193       203       213    || 227       237       247       257       267       277       287       297       307       317       327       337       347         
                                                                                                                             103-CSD                                       149|            180|                             218|                                                                                                                                     
                                                                                                                                                                            165             186                              223
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LRX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LRX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LRX)

(-) Gene Ontology  (157, 165)

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  5lrx
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TNAP3_HUMAN | P21580: 2eqe 2eqf 2eqg 2vfj 3dkb 3oj3 3oj4 3vuw 3vux 3vuy 3zjd 3zje 3zjf 3zjg 4zrh 4zs5 5dod
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(-) Related Entries Specified in the PDB File

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