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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OTU DOMAIN OF GUMBY/FAM105B AT 1.6 ANGSTROM
 
Authors :  D. F. Ceccarelli, Y. -C. Juang, F. Sicheri
Date :  17 May 13  (Deposition) - 05 Jun 13  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Otu Domain, Deubiquitinase, Ubiquitin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rivkin, S. M. Almeida, D. F. Ceccarelli, Y. -C. Juang, T. A. Maclean, T. Srikumar, H. Huang, W. Dunham, R. Fukumura, G. Xie, Y. Gondo, B. Raught, A. -C. Gingras, F. Sicheri, S. Cordes
The Linear Ubiquitin-Specific Deubiquitinase Gumby Regulate Angiogenesisthe Linear Ubiquitin-Specific Deubiquitinase Gumby Regulates Angiogenesis
Nature 2013
PubMed: search  |  Reference-DOI: 10.1038/NATURE12296

(-) Compounds

Molecule 1 - PROTEIN FAM105B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PROEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: OTU DOMAIN (UNP RESIDUES 79-352)
    Gene: FAM105B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2GOL2Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:92 , LYS A:93 , LYS A:107 , GLU A:111BINDING SITE FOR RESIDUE BME A 401
2AC2SOFTWARETRP A:167 , ASP A:268 , GLY A:270 , GLN A:271 , ARG A:274BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREHIS A:276 , GLY A:284 , GLY A:285 , GLU A:287 , GLU A:290BINDING SITE FOR RESIDUE GOL A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KSJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KSJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhhhhh...hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhh.eeeeee.hhh.hhh.eeee.........eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ksj A  78 SRLSVAPEmDImDYCKKEWRGNTQKATCmKmGYEEVSQKFTSIRRVRGDNYCALRATLFQAmSQAVGLPPWLQDPELmLLPEKLISKYNWIKQWKLDLVDKIKESLTLLRKKWAGLAEmRTAEARQIACDELFTNEAEEYSLYEAVKFLmLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEmFLLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEDDRHYNIPVR 345
                                    87 |      97       107|      117       127       137 |     147       157       167     ||186       196       206       216       226       236       246       256       266       276       286    |  296       306       316       326       336         
                                   86-MSE             106-MSE                          139-MSE         155-MSE           173|                   205-MSE                        236-MSE                                                291-MSE                                                  
                                      89-MSE            108-MSE                                                           183
   Legend:   → Mismatch (orange background)
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  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 4KSJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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    Tyr A:319 - Pro A:320   [ RasMol ]  
 

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  OTUL_HUMAN | Q96BN8
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 Related Entries

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

UniProtKB/Swiss-Prot
        OTUL_HUMAN | Q96BN8: 3znv 3znx 3znz 4ksk 4ksl 4oyk 4p0b

(-) Related Entries Specified in the PDB File

4ksk 4ksl