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(-) Description

Title :  HUMAN UBIQUITIN-ACTIVATING ENZYME 5 IN COMPLEX WITH AMPPNP
 
Authors :  J. R. Walker, J. P. Bacik, Y. Li, J. Weigelt, C. Bountra, C. H. Arrowsmith A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics C (Sgc)
Date :  29 Mar 09  (Deposition) - 26 May 09  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Atp-Binding, Ubl Conjugation Pathway, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, J. P. Bacik, Y. Li, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Human Ubiquitin-Activating Enzyme 5 In Complex With Amppnp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 5
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBA5, UBE1DC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-ACTIVATING ENZYME 5, UBIQUITIN-ACTIVATING ENZYME E1 DOMAIN-CONTAINING PROTEIN 1, UFM1-ACTIVATING ENZYME, THIFP1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:226 , CYS A:229 , CYS A:303 , CYS A:308BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREGLY A:80 , GLY A:82 , GLY A:83 , VAL A:84 , ASP A:104 , TYR A:105 , ASP A:106 , LYS A:127 , ASN A:150 , ILE A:151 , THR A:152 , CYS A:181 , VAL A:182 , ASP A:183 , ASN A:184 , ALA A:187 , VAL A:207 , HOH A:427 , HOH A:463BINDING SITE FOR RESIDUE ANP A 402
3AC3SOFTWARECYS B:226 , CYS B:229 , CYS B:303 , CYS B:308BINDING SITE FOR RESIDUE ZN B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077155G168EUBA5_HUMANDisease (EIEE44)  ---A/BG168E
2UniProtVAR_077156V260MUBA5_HUMANDisease (EIEE44)  ---A/BV260M
3UniProtVAR_077157K310EUBA5_HUMANDisease (SCAR24)  ---A/BK310E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GUC)

(-) 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:242
 aligned with UBA5_HUMAN | Q9GZZ9 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:261
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
           UBA5_HUMAN    69 EKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVAANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKVAALPKQEVIQ 329
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee..hhhhhhhhhhhhhhh..eeeee......--------.hhhhh..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh.........eeee...hhhhhhhhhhhhhhhh..eeeeee.....eeeeeee.................---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......ee.........hhhhhhhhhhhhhhhh..--..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------M-------------------------------------------------E------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3guc A  69 EKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVE--------FQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVA---------REGVCAASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKVAAL--QEVIQ 329
                                    78        88        98       108|      118       128       138       148       158       168       178       188       198       208       218       228       | -       248       258       268       278       288       298       308       318   |  |328 
                                                                  109      118                                                                                                                   236       246                                                                         322  |    
                                                                                                                                                                                                                                                                                          325    

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with UBA5_HUMAN | Q9GZZ9 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:251
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318 
           UBA5_HUMAN    69 EKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVAANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKV 319
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee...hhhhhhhhhhhhh...eeeee...------------------.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh.........eeee...hhhhhhhhhhhhhhhh..eeeeee.....eeeeeee...................------------.hhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......ee.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------M-------------------------------------------------E--------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3guc B  69 EKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYD------------------LSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVAAN------------AASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKV 319
                                    78        88        98       | -         -      |128       138       148       158       168       178       188       198       208       218       228       238         -  |    258       268       278       288       298       308       318 
                                                               106                125                                                                                                              238          251                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UBA5_HUMAN | Q9GZZ9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0071566    UFM1 activating enzyme activity    Catalysis of the activation of the small ubiquitin-related modifier UFM1, through the formation of an ATP-dependent high-energy thiolester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
    GO:0061503    tRNA threonylcarbamoyladenosine dehydratase    Catalysis of the ATP-dependent dehydration of t6A to form cyclic t6A.
biological process
    GO:0061504    cyclic threonylcarbamoyladenosine biosynthetic process    The chemical reactions and pathways resulting in the formation of cyclic threonylcarbamoyladenosine, a modified nucleoside found in some tRNA molecules.
    GO:1990592    protein K69-linked ufmylation    A protein ufmylation process in which a polymer of the ubiquitin-like protein UFM1 is formed by linkages between lysine residues at position 69 of the UFM1 monomers, is added to a protein.
    GO:0071569    protein ufmylation    Covalent attachment of the ubiquitin-like protein UFM1 to another protein.
    GO:0033146    regulation of intracellular estrogen receptor signaling pathway    Any process that modulates the frequency, rate or extent of the activity of an intracellular estrogen receptor signaling pathway.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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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        UBA5_HUMAN | Q9GZZ93h8v 5hkh 5ia8 5iaa 5l95

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