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(-) Description

Title :  REVISITED CRYO-EM STRUCTURE OF INDUCIBLE LYSINE DECARBOXYLASE COMPLEXED WITH LARA DOMAIN OF RAVA ATPASE
 
Authors :  E. Kandiah, D. Carriel, J. Perard, H. Malet, M. Bacia, K. Liu, S. W. S. Cha W. A. Houry, S. Ollagnier De Choudens, S. Elsen, I. Gutsche
Date :  21 Oct 15  (Deposition) - 21 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  6.20
Chains :  Asym. Unit :  A,K
Biol. Unit 1:  A,K  (10x)
Keywords :  Hydrolase-Isomerase Complex, Acid-Stress, Atpase, Rava (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Kandiah, D. Carriel, J. Perard, H. Malet, M. Bacia, K. Liu, S. W. S. Chan, W. A. Houry, S. Ollagnier De Choudens, S. Elsen, I. Gutsche
Structural Insights Into The Escherichia Coli Lysine Decarboxylases And Molecular Determinants Of Interaction With The Aaa+ Atpase Rava.
Sci. Rep. V. 6 24601 2016
PubMed-ID: 27080013  |  Reference-DOI: 10.1038/SREP24601
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSINE DECARBOXYLASE, INDUCIBLE
    Chains: A
    EC Number: 4.1.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655
    Expression System Taxid: 511145
    Expression System Vector: PET22B
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: LDC, LDC, INDUCIBLE LYSINE DECARBOXYLASE
 
Molecule 2 - ATPASE RAVA
    Chains: K
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: P11
    Expression System Vector Type: PLASMID
    Fragment: LARA DOMAIN OF RAVA ATPASE
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: REGULATORY ATPASE VARIANT A, REGULATORY ATPASE VARIANT A, R AVA ATPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AK
Biological Unit 1 (10x): AK

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FL2)

(-) Sites  (0, 0)

(no "Site" information available for 5FL2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FL2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:149 -Pro A:150
2Asn A:305 -Ser A:306
3Tyr A:652 -Pro A:653
4Pro A:653 -Pro A:654

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FL2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FL2)

(-) 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:710
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh....eeee.......hhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeee...............hhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhh...eeeee.....hhhhhhhhh.............eeeeeee..........eeeeee...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...........ee..................ee...eeeee...............hhhhhhhhhhhh.....eee..eeeee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhh..eeeee.hhh.........eee..........ee....hhhhhhhhhhhhhhh........eee.eee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fl2 A   1 MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEEISKMNENLPLYAFANTYSTLDVSLNDLRLQISFFEYALGAAEDIANKIKQTTDEYINTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSLFYDFFGPNTMKSDISISVSELGSLLDHSGPHKEAEQYIARVFNADRSYMVTNGTSTANKIVGMYSAPAGSTILIDRNCHKSLTHLMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTYDGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTHLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTSPHYGIVASTETAAAMMKGNAGKRLINGSIERAIKFRKEIKRLRTESDGWFFDVWQPDHIDTTECWPLRSDSTWHGFKNIDNEHMYLDPIKVTLLTPGMEKDGTMSDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKNMLPSLYREDPEFYENMRIQELAQNIHKLIVHHNLPDLMYRAFEVLPTMVMTPYAAFQKELHGMTEEVYLDEMVGRINANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLKE 711
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     ||371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711
                                                                                                                                                                                                                                                                                                                                                                                                       366|                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                        368                                                                                                                                                                                                                                                                                                                                                       


Chain K from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.........ee.........eeeeeeeeeeee..eeeeeeeeehhhhhhhhhhh...eeee.....eee.eeee.....eeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5fl2 K 332 DKTALTVIRLGGIFSRRQQYQLPVNVTASTLTLLLQKPLKLHDMEVVHISFERSALEQWLSKGGEIRGKLNGIGFAQKLNLEVDSAQHLVVRDVSLQGSTLALPGS 437
                                   341       351       361       371       381       391       401       411       421       431
   Legend:   → Mismatch (orange background)
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  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 5FL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FL2)

(-) Gene Ontology  (16, 19)

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  Cis Peptide Bonds
    Asn A:305 - Ser A:306   [ RasMol ]  
    Pro A:653 - Pro A:654   [ RasMol ]  
    Thr A:149 - Pro A:150   [ RasMol ]  
    Tyr A:652 - Pro A:653   [ RasMol ]  
 
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  RAVA_ECOLI | P31473
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDCI_ECOLI | P0A9H3: 3n75 3q16 4upb 4upf 5fkx
        RAVA_ECOLI | P31473: 3nbx 4upb 4upf

(-) Related Entries Specified in the PDB File

5fkx STRUCTURE OF E.COLI INDUCIBLE LYSINE DECARBOXYLASE AT ACTIVE PH
5fkz STRUCTURE OF E.COLI CONSTITUTIVE LYSINE DECARBOXYLASE RELATED ID: EMD-3206 RELATED DB: EMDB