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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI RAVA (REGULATORY ATPASE VARIANT A) IN COMPLEX WITH ADP
 
Authors :  M. El Bakkouri
Date :  04 Jun 10  (Deposition) - 12 Jan 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym./Biol. Unit :  X
Keywords :  Aaa+ Atpase, Alpha-Beta-Alpha Structure, Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. El Bakkouri, I. Gutsche, U. Kanjee, B. Zhao, M. Yu, G. Goret, G. Schoehn, W. P. Burmeister, W. A. Houry
Structure Of Rava Moxr Aaa+ Protein Reveals The Design Principles Of A Molecular Cage Modulating The Inducible Lysine Decarboxylase Activity
Proc. Natl. Acad. Sci. Usa V. 107 22499 2010
PubMed-ID: 21148420  |  Reference-DOI: 10.1073/PNAS.1009092107

(-) Compounds

Molecule 1 - ATPASE RAVA
    Chains: X
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B3746, JW3725, RAVA, YIEN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12 MG1655
    Synonym: REGULATORY ATPASE VARIANT A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY X:21 , TYR X:23 , GLY X:49 , ILE X:50 , ALA X:51 , LYS X:52 , SER X:53 , LEU X:54 , ARG X:170 , VAL X:180 , MET X:189 , GLU X:196 , ARG X:251 , LYS X:254 , HOH X:537BINDING SITE FOR RESIDUE ADP X 800
2AC2SOFTWAREARG X:398 , LYS X:409 , GLN X:468 , LYS X:469BINDING SITE FOR RESIDUE SO4 X 499

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NBX)

(-) 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 X from PDB  Type:PROTEIN  Length:481
 aligned with RAVA_ECOLI | P31473 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:495
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492     
           RAVA_ECOLI     3 HPHLLAERISRLSSSLEKGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQASAFFSGRSAVAPVDLILLKDCLWYDAQSLNLIQQQIDVLMTGHAWQQQGMLTRLGAIVQRHLQLQQQQSDKTALTVIRLGGIFSRRQQYQLPVNVTASTLTLLLQKPLKLHDMEVVHISFERSALEQWLSKGGEIRGKLNGIGFAQKLNLEVDSAQHLVVRDVSLQGSTLALPGSSAEGLPGEIKQQLEELESDWRKQHALFSEQQKCLFIPGDWLGRIEASLQDVGAQIRQAQQ 497
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------AAA_5-3nbxX01 X:41-171                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    DUF3763-3nbxX02 X:442-497                                Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh....eeeee.....hhhhhhh...----------......hhhhh.eeeee.hhhhhhhhhhhhhhhhhh.eee....eee....eeeeee.........hhhhhh...eeee.....hhhhhhhhhh................hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........ee.........ee.........eeeeeeeeeeee..eeeeeeeeehhhhhhhhhhh...eeee.....eee.eeee.....eeee.....eeeee....----.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nbx X   3 HPHLLAERISRLSSSLEKGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLS----------ERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQASAFFSGRSAVAPVDLILLKDCLWYDAQSLNLIQQQIDVLMTGHAWQQQGMLTRLGAIVQRHLQLQQQQSDKTALTVIRLGGIFSRRQQYQLPVNVTASTLTLLLQKPLKLHDMEVVHISFERSALEQWLSKGGEIRGKLNGIGFAQKLNLEVDSAQHLVVRDVSLQGSTLALPGS----LPGEIKQQLEELESDWRKQHALFSEQQKCLFIPGDWLGRIEASLQDVGAQIRQAQQ 497
                                    12        22        32        42        52        62        72        82    |    -     | 102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432    |  442       452       462       472       482       492     
                                                                                                               87         98                                                                                                                                                                                                                                                                                                                                                437  442
   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 3NBX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: DUF3763] (1)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (RAVA_ECOLI | P31473)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAVA_ECOLI | P31473: 4upb 4upf 5fl2

(-) Related Entries Specified in the PDB File

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