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(-) Description

Title :  E2 BINDING SURFACE ON UBA3 BETA-GRASP DOMAIN UNDERGOES A CONFORMATIONAL TRANSITION
 
Authors :  E. S. Elgin, F. C. Peterson, B. F. Volkman
Date :  27 Feb 12  (Deposition) - 25 Jul 12  (Release) - 28 Aug 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  E1 Enzyme, Beta Grasp Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. S. Elgin, N. Sokmen, F. C. Peterson, B. F. Volkman, C. Dag, A. L. Haas
E2-Binding Surface On Uba3 Beta-Grasp Domain Undergoes A Conformational Transition.
Proteins V. 80 2482 2012
PubMed-ID: 22821745  |  Reference-DOI: 10.1002/PROT.24148

(-) Compounds

Molecule 1 - NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainSG13009[PREP4]
    Expression System Taxid562
    Expression System VectorPQE30
    FragmentINTERACTION WITH UBE2M CORE DOMAIN RESIDUES 368-463
    GeneUBA3, UBE1C
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDD8-ACTIVATING ENZYME E1C, UBIQUITIN-ACTIVATING ENZYME E1C, UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 3, UBIQUITIN- ACTIVATING ENZYME 3

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2LQ7)

(-) Sites  (0, 0)

(no "Site" information available for 2LQ7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LQ7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LQ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LQ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2LQ7)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003610551aENSE00001864869chr3:69129559-6912948575UBA3_HUMAN1-770--
1.2aENST000003610552aENSE00001417479chr3:69129304-6912926342UBA3_HUMAN7-21150--
1.3aENST000003610553aENSE00000966869chr3:69127069-69126949121UBA3_HUMAN21-61410--
1.4aENST000003610554aENSE00001377164chr3:69124661-6912458181UBA3_HUMAN62-88270--
1.5aENST000003610555aENSE00001376644chr3:69120768-6912068683UBA3_HUMAN89-116280--
1.6ENST000003610556ENSE00000966872chr3:69117159-6911707981UBA3_HUMAN116-143280--
1.7aENST000003610557aENSE00000966873chr3:69113262-6911321944UBA3_HUMAN143-158160--
1.8ENST000003610558ENSE00000966874chr3:69112654-6911259065UBA3_HUMAN158-179220--
1.9ENST000003610559ENSE00000966875chr3:69112288-69112133156UBA3_HUMAN180-231520--
1.10ENST0000036105510ENSE00000966876chr3:69111330-69111228103UBA3_HUMAN232-266350--
1.11aENST0000036105511aENSE00000966877chr3:69111078-69110965114UBA3_HUMAN266-304390--
1.12ENST0000036105512ENSE00000966878chr3:69106460-6910640754UBA3_HUMAN304-322190--
1.13ENST0000036105513ENSE00001656120chr3:69105966-6910593037UBA3_HUMAN322-334130--
1.14ENST0000036105514ENSE00001685710chr3:69105844-6910576382UBA3_HUMAN334-361280--
1.15ENST0000036105515ENSE00001754233chr3:69105434-69105334101UBA3_HUMAN362-395341A:346-37429
1.16ENST0000036105516ENSE00001711956chr3:69105214-6910515164UBA3_HUMAN395-416221A:374-39522
1.17ENST0000036105517ENSE00001673741chr3:69105056-6910500255UBA3_HUMAN417-435191A:396-41419
1.18bENST0000036105518bENSE00001518240chr3:69104676-69103881796UBA3_HUMAN435-463291A:414-44229

(-) Sequences/Alignments

NMR Structure
   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:97
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:97
                                   376       386       396       406       416       426       436       446       456       
           UBA3_HUMAN   367 CSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS 463
               SCOP domains d2lq7a_ A: UBA3                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhh..........eeeeee..eeee.............hhhhhh..........eeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15  PDB: A:346-374    ---------------------Exon 1.17          ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.16             ------------------Exon 1.18b  PDB: A:414-442    Transcript 1 (2)
                 2lq7 A 346 GSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS 442
                                   355       365       375       385       395       405       415       425       435       

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LQ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LQ7)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (UBA3_HUMAN | Q8TBC4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0007113    endomitotic cell cycle    A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    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: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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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UBA3_HUMAN | Q8TBC41r4m 1r4n 1tt5 1y8x 1yov 2nvu 3dbh 3dbl 3dbr 3fn1 3gzn 5jjm

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