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(-) Description

Title :  CRYSTAL STRUCTURE OF TRICHINELLA SPIRALIS UCH37 CATALYTIC DOMAIN BOUND TO UBIQUITIN VINYL METHYL ESTER
 
Authors :  M. E. Morrow, J. A. Ronau, R. R. White, K. Artavanis-Tsakonas, C. Das
Date :  29 Nov 12  (Deposition) - 29 May 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Beta-Helix Sandwich, Protein-Protein Complex, Deubiquitination, Ubiquitin C-Terminal Hydrolase, Cytosol, Hydrolase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Morrow, M. I. Kim, J. A. Ronau, M. J. Sheedlo, R. R. White, J. Chaney L. N. Paul, M. A. Lill, K. Artavanis-Tsakonas, C. Das
Stabilization Of An Unusual Salt Bridge In Ubiquitin By The Extra C-Terminal Domain Of The Proteasome-Associated Deubiquitinase Uch37 As A Mechanism Of Its Exo Specificity.
Biochemistry V. 52 3564 2013
PubMed-ID: 23617878  |  Reference-DOI: 10.1021/BI4003106

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-HYDROLASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN RESIDUES 1-226
    Organism Common: TRICHINA WORM
    Organism Scientific: TRICHINELLA SPIRALIS
    Organism Taxid: 6334
 
Molecule 2 - UBIQUITIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UBC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GVE2Ligand/IonMETHYL 4-AMINOBUTANOATE
3MSE10Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GVE1Ligand/IonMETHYL 4-AMINOBUTANOATE
3MSE5Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1DTT-1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GVE1Ligand/IonMETHYL 4-AMINOBUTANOATE
3MSE5Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:114 , LEU A:125 , CYS A:126 , ASN A:129BINDING SITE FOR RESIDUE DTT A 301
2AC2SOFTWAREHIS A:99 , VAL A:102 , HOH A:443 , HOH A:463 , HOH A:511BINDING SITE FOR RESIDUE NA A 302
3AC3SOFTWARELEU A:8 , GLN A:79 , GLN A:82 , CYS A:85 , LEU A:154 , VAL A:159 , PHE A:160 , HIS A:161 , LEU A:178 , GLY B:75BINDING SITE FOR RESIDUE GVE B 101
4AC4SOFTWARELEU C:8 , GLN C:79 , GLN C:82 , CYS C:85 , VAL C:159 , PHE C:160 , HIS C:161 , LEU C:178 , GLY D:75BINDING SITE FOR RESIDUE GVE D 101

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:71 -C:71

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:44 -Pro A:45
2Ala A:189 -Ser A:190
3Gly C:-1 -Ser C:0
4Lys C:44 -Pro C:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I6N)

(-) Exons   (0, 0)

(no "Exon" information available for 4I6N)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains d4i6na_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......ee.hhhhhhhhhhhh....eeeeee......hhhhh.eeeeeeeee.hhhhhhh....hhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh..eeeeeeeee..eeeee.......eeeee.....hhhhhhhhhhhhhhh.........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6n A  -3 PLGSmAEGNWCLIESDPGIFTEmIHGFGCTGLQVEELVVLDESIEHLKPIHGFIFLFRWLKKEmRKEVDDSPQTCTDVYFSQQVIQNACASQALINLLLNCDHPDVDLGPTLKEFKDFTYDLDSASRGLCLTNSEKIRAVHNSFGQKLDEEDVFHFVTYVPVNDGVYELDGLRAAPLRLGTVASDGDWTEVAIKAIKEKIKNYGESEVRFNLmAVISDQ 225
                                |    6        16  |     26        36        46        56   |    66        76        86        96       106       116       126       136    || 156       166       176       186       196       206       216  |      
                                |                19-MSE                                   60-MSE                                                                          141|                                                                219-MSE  
                                1-MSE                                                                                                                                      152                                                                         


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4i6nb_ B: Ubiquitin                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4i6n B   1 mQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                            |       10        20        30        40        50        60        70     
                            1-MSE                                                                      


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4i6nc_ C: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.hhhhhhhhhhhh....eeeeee......hhhhh.eeeeeeeee.hhhhhhh....hhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeee.......eeeee......hhhhhhhhhhhhhhh.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6n C  -3 PLGSmAEGNWCLIESDPGIFTEmIHGFGCTGLQVEELVVLDESIEHLKPIHGFIFLFRWLKKEmRKEVDDSPQTCTDVYFSQQVIQNACASQALINLLLNCDHPDVDLGPTLKEFKDFTYDLDSASRGLCLTNSEKIRAVHNSFGKLDEEDVFHFVTYVPVNDGVYELDGLRAAPLRLGTVASDGDWTEVAIKAIKEKIKNYGESEVRFNLmAVISD 224
                                |    6        16  |     26        36        46        56   |    66        76        86        96       106       116       126       136    || 157       167       177       187       197       207       217 |     
                                1-MSE            19-MSE                                   60-MSE                                                                          141|                                                               219-MSE 
                                                                                                                                                                           153                                                                       


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4i6nd_ D: Ubiquitin                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4i6n D   1 mQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                            |       10        20        30        40        50        60        70     
                            1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I6N)

(-) Gene Ontology  (87, 87)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc
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        E5S6X1_TRISP | E5S6X1: 4ig7

(-) Related Entries Specified in the PDB File

3ihr STRUCTURE OF FULL-LENGTH, HUMAN PROTEIN