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(-) Description

Title :  THE PLECKSTRIN HOMOLOGY (PH) DOMAIN OF USP37
 
Authors :  A. Dong, U. B. Nair, A. Wernimont, J. R. Walker, J. Weigelt, C. Bountra, A. M. Edwards, C. H. Arrowsmith, S. Dhe-Paganon, Structural Genomic Consortium (Sgc)
Date :  29 Sep 11  (Deposition) - 09 Nov 11  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Ph-Domain, Hydrolase, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Dong, U. B. Nair, A. Wernimont, J. R. Walker, J. Weigelt, C. Bountra, A. M. Edwards, C. H. Arrowsmith, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
The Pleckstrin Homology (Ph) Domain Of Usp37
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - USP37 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 4-125
    GeneUSP37
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 42)

Asymmetric Unit (5, 42)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
5UNX29Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3MSE3Mod. Amino AcidSELENOMETHIONINE
4SO43Ligand/IonSULFATE ION
5UNX21Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (5, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
5UNX8Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , GLN A:77 , ASN A:105BINDING SITE FOR RESIDUE SO4 A 1000
2AC2SOFTWARELYS A:35 , GLN A:52 , HOH A:161BINDING SITE FOR RESIDUE SO4 A 1003
3AC3SOFTWARETHR A:20 , LYS A:21 , EDO B:2010BINDING SITE FOR RESIDUE SO4 A 1004
4AC4SOFTWAREPRO A:9 , TRP A:22 , ASP A:85BINDING SITE FOR RESIDUE ACT A 1501
5AC5SOFTWAREGLN B:52 , HOH B:167BINDING SITE FOR RESIDUE EDO B 2012
6AC6SOFTWARESO4 A:1004 , ASN B:59 , VAL B:60 , HIS B:103 , HOH B:138BINDING SITE FOR RESIDUE EDO B 2010
7AC7SOFTWAREHIS B:55 , GLN B:77 , ASN B:105 , HOH B:162BINDING SITE FOR RESIDUE SO4 B 1001
8AC8SOFTWARELEU B:4 , LYS B:5 , ILE B:6 , ASP B:91 , GLU B:94BINDING SITE FOR RESIDUE ACT B 1502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U12)

(-) Exons   (0, 0)

(no "Exon" information available for 3U12)

(-) 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:104
 aligned with Q86W68_HUMAN | Q86W68 from UniProtKB/TrEMBL  Length:302

    Alignment length:104
                                    12        22        32        42        52        62        72        82        92       102    
         Q86W68_HUMAN     3 PLKIHGPIRIRSMQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLMLTLQDNSFLSIDKVPSKDAEEMRLFLDAVHQNR 106
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...ee...eeeeeeeeee..eeeeeeee......eeee....eeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3u12 A   3 SLKIHGPIRIRSmQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLmLTLQDNSFLSIDKVPSKDAEEmRLFLDAVHQNR 106
                                    12  |     22        32        42        52        62        72|       82        92  |    102    
                                       15-MSE                                                    73-MSE                95-MSE       

Chain A from PDB  Type:PROTEIN  Length:104
 aligned with UBP37_HUMAN | Q86T82 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:104
                                    12        22        32        42        52        62        72        82        92       102    
          UBP37_HUMAN     3 PLKIHGPIRIRSMQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLMLTLQDNSFLSIDKVPSKDAEEMRLFLDAVHQNR 106
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...ee...eeeeeeeeee..eeeeeeee......eeee....eeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3u12 A   3 SLKIHGPIRIRSmQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLmLTLQDNSFLSIDKVPSKDAEEmRLFLDAVHQNR 106
                                    12  |     22        32        42        52        62        72|       82        92  |    102    
                                       15-MSE                                                    73-MSE                95-MSE       

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with Q86W68_HUMAN | Q86W68 from UniProtKB/TrEMBL  Length:302

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
         Q86W68_HUMAN     2 SPLKIHGPIRIRSMQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLMLTLQDNSFLSIDKVPSKDAEEMRLFLDAVHQNRL 107
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.---.....eeeeeeeeee..eeeeeeee......eeee....eeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3u12 B   2 GSLKIHGPIRIRS---GITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLmLTLQDNSFLSIDKVPSKDAEEmRLFLDAVHQNRL 107
                                    11  |   | 21        31        41        51        61        71 |      81        91   |   101      
                                       14  18                                                     73-MSE                95-MSE        

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with UBP37_HUMAN | Q86T82 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
          UBP37_HUMAN     2 SPLKIHGPIRIRSMQTGITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLMLTLQDNSFLSIDKVPSKDAEEMRLFLDAVHQNRL 107
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.---.....eeeeeeeeee..eeeeeeee......eeee....eeeeeeee....eeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3u12 B   2 GSLKIHGPIRIRS---GITKWKEGSFEIVEKENKVSLVVHYNTGGIPRIFQLSHNIKNVVLRPSGAKQSRLmLTLQDNSFLSIDKVPSKDAEEmRLFLDAVHQNRL 107
                                    11  |   | 21        31        41        51        61        71 |      81        91   |   101      
                                       14  18                                                     73-MSE                95-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  (0, 0)

(no "SCOP Domain" information available for 3U12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U12)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBP37_HUMAN | Q86T82)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0035871    protein K11-linked deubiquitination    A protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein.
    GO:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain A,B   (Q86W68_HUMAN | Q86W68)

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