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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN
 
Authors :  W. -C. Huang, T. -P. Ko, S. S. -L. Li, A. H. -J. Wang
Date :  02 Jul 04  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Ubiquitin Fold, Half-Open Barrel, Two Helices, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. -C. Huang, T. -P. Ko, S. S. -L. Li, A. H. -J. Wang
Crystal Structures Of The Human Sumo-2 Protein At 1. 6 A And 1. 2 A Resolution: Implication On The Functional Differences Of Sumo Proteins
Eur. J. Biochem. V. 271 4114 2004
PubMed-ID: 15479240  |  Reference-DOI: 10.1111/J.1432-1033.2004.04349.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN SMT3B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: NO N-TERMINAL ARM(RESIDUES 12-89)
    Gene: SUMO-2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUMO-2, SMALL UBIQUITIN-LIKE MODIFIER, SENTRIN 2, HSMT3
    Tissue: BRAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WM2)

(-) Sites  (0, 0)

(no "Site" information available for 1WM2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047508D16NSUMO2_HUMANPolymorphism17850328AD16N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047508D16NSUMO2_HUMANPolymorphism17850328AD16N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SUMO2_HUMAN16-93  1A:16-89
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SUMO2_HUMAN16-93  3A:16-89

(-) Exons   (0, 0)

(no "Exon" information available for 1WM2)

(-) 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    
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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:78
 aligned with SUMO2_HUMAN | P61956 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:78
                                    21        31        41        51        61        71        81        
           SUMO2_HUMAN   12 TENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQ 89
               SCOP domains d1wm2a_ A: SUMO-2                                                              SCOP domains
               CATH domains 1wm2A00 A:12-89                                                                CATH domains
               Pfam domains ------Rad60-SLD-1wm2A01 A:18-88                                              - Pfam domains
         Sec.struct. author .....eeeeeeee....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----N------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----UBIQUITIN_2  PDB: A:16-89 UniProt: 16-93                                   PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                  1wm2 A 12 TENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQ 89
                                    21        31        41        51        61        71        81
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  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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (SUMO2_HUMAN | P61956)
molecular function
    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:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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  1wm2
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  SUMO2_HUMAN | P61956
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 Related Entries

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

UniProtKB/Swiss-Prot
        SUMO2_HUMAN | P61956: 1wm3 1wz0 1z5q 2awt 2ckh 2d07 2io0 2io3 2iyd 2n1w 2n9e 2rpq 3uin 3uio 3zo5 4bkg 4npn 5d2m 5elu 5eql 5ghb 5ghc

(-) Related Entries Specified in the PDB File

1wm3 THE SAME PROTEIN AT 1.2 A