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(-) Description

Title :  THE CRYSTAL STRUCTURE OF P18, HUMAN TRANSLATION ELONGATION FACTOR 1 EPSILON 1
 
Authors :  B. S. Kang, K. J. Kim, M. H. Kim, Y. S. Oh, S. Kim
Date :  26 Apr 07  (Deposition) - 25 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Biosynthesis, Aminoacyl-Trna Synthetase, P18, Gst, Nuclear Protein, Elongation Factor, Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. J. Kim, M. C. Park, S. J. Choi, Y. S. Oh, E. C. Choi, H. J. Cho, M. H. Kim, S. H. Kim, D. W. Kim, S. Kim, B. S. Kang
Determination Of Three-Dimensional Structure And Residues Of The Novel Tumor Suppressor Aimp3/P18 Required For The Interaction With Atm.
J. Biol. Chem. V. 283 14032 2008
PubMed-ID: 18343821  |  Reference-DOI: 10.1074/JBC.M800859200

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX-HTA
    Expression System StrainB834
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsFIVE RESIDUES AT C-TERMINUS ARE DELETED
    SynonymEUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON 1, MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P18, ELONGATION FACTOR P18

 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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:136 , LEU A:140 , PHE A:164 , ILE A:165 , HOH A:2060 , HOH A:2075 , HOH A:2078BINDING SITE FOR RESIDUE GOL A1171
2AC2SOFTWARELYS B:136 , LEU B:140 , ILE B:165 , HOH B:2051 , HOH B:2073 , HOH B:2074 , HOH B:2075BINDING SITE FOR RESIDUE GOL B1171

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UZ8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:37 -Gly A:38
2Asn B:37 -Gly B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UZ8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.MCA3_HUMAN50-173
 
  2A:50-170
B:50-170
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.MCA3_HUMAN50-173
 
  1A:50-170
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.MCA3_HUMAN50-173
 
  1-
B:50-170

(-) Exons   (0, 0)

(no "Exon" information available for 2UZ8)

(-) 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:166
 aligned with MCA3_HUMAN | O43324 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
           MCA3_HUMAN     1 MAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRLY 170
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh........eee....eeeee.....eeehhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------GST_CTER  PDB: A:50-170 UniProt: 50-173                                                                                   PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz8 A   1 mAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLmGLTTIAAHLVKQANKEYLLGSTAEEKAmVQQWLEYRVTQVDG----NDIHTLLmDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRLY 170
                            |       10        20        30        40 |      50        60        70        80   |    90     | 100       110       120       130       140       150       160       170
                            |                                       42-MSE                      70-MSE        84   89     96-MSE                                                                      
                            1-MSE                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MCA3_HUMAN | O43324 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
           MCA3_HUMAN     1 MAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRLY 170
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------GST_C-2uz8B01 B:67    -153                                                             ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------GST_C-2uz8B02 B:67    -153                                                             ----------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh.......eeee....eeeee.....eeehhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh...----.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------GST_CTER  PDB: B:50-170 UniProt: 50-173                                                                                   PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz8 B   1 mAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLmGLTTIAAHLVKQANKEYLLGSTAEEKAmVQQWLEYRVTQVDG----NDIHTLLmDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRLY 170
                            |       10        20        30        40 |      50        60        70        80   |    90     | 100       110       120       130       140       150       160       170
                            1-MSE                                   42-MSE                      70-MSE        84   89     96-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 2UZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2UZ8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GST_C (118)
(-)
Family: GST_C (102)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCA3_HUMAN | O43324)
molecular function
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    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:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0043517    positive regulation of DNA damage response, signal transduction by p53 class mediator    Any process that activates, maintains or increases the rate of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2000774    positive regulation of cellular senescence    Any process that activates or increases the frequency, rate or extent of cellular senescence.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        MCA3_HUMAN | O433244bl7 4bvx 4bvy 5bmu

(-) Related Entries Specified in the PDB File

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