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(-) Description

Title :  CRYSTAL STRUCTURE OF LON PROTEASE FROM THERMOCOCCUS ONNURINEUS NA1
 
Authors :  S. S. Cha, Y. J. An
Date :  28 Sep 09  (Deposition) - 22 Sep 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Atp-Dependent Protease, Atp-Binding, Nucleotide-Binding, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Cha, Y. J. An, C. R. Lee, H. S. Lee, Y. G. Kim, S. J. Kim, K. K. Kwon, G. M. De Donatis, J. H. Lee, M. R. Maurizi, S. G. Kang
Crystal Structure Of Lon Protease: Molecular Architecture O Gated Entry To A Sequestered Degradation Chamber
Embo J. V. 29 3520 2010
PubMed-ID: 20834233  |  Reference-DOI: 10.1038/EMBOJ.2010.226

(-) Compounds

Molecule 1 - ATP-DEPENDENT PROTEASE LON
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: THERMOCOCCUS ONNURINEUS
    Organism Taxid: 523850
    Strain: NA1
    Synonym: LON PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
3PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
2PE43Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
3PE83Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:42 , VAL A:43 , ILE A:44 , GLY A:70 , THR A:71 , GLY A:72 , LYS A:73 , SER A:74 , MET A:75 , PHE A:338 , GLU A:342 , ARG A:345 , LEU A:378 , ARG A:379 , HOH A:672 , HOH A:772 , HOH A:830 , HOH A:908 , HOH A:914 , TYR B:315 , HOH B:867BINDING SITE FOR RESIDUE ADP A 642
2AC2SOFTWARETYR A:423 , LYS A:427 , ILE A:455 , GLN A:514 , THR A:515 , TYR A:516 , GLU A:517 , GLY A:518BINDING SITE FOR RESIDUE PE8 A 643
3AC3SOFTWARETYR A:516 , HOH B:150 , ILE B:560BINDING SITE FOR RESIDUE PE4 A 644
4AC4SOFTWAREVAL B:43 , ILE B:44 , GLY B:70 , THR B:71 , GLY B:72 , LYS B:73 , SER B:74 , MET B:75 , GLU B:342 , ARG B:345 , LEU B:378 , ARG B:379 , HOH B:679 , HOH B:818 , HOH B:836 , HOH B:984BINDING SITE FOR RESIDUE ADP B 642

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:112 -A:189
2B:112 -B:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K1J)

(-) Exons   (0, 0)

(no "Exon" information available for 3K1J)

(-) 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:566
 aligned with B6YU74_THEON | B6YU74 from UniProtKB/TrEMBL  Length:635

    Alignment length:618
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627        
         B6YU74_THEON    18 GESLELGIEFTTTEEIEVPEKLIDQVIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVPACQGRRIVEKYREKAKSQESVKSYILLFVMFTVMLALFIEFSATTLLMGLFVVILTIMALSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHERVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMAKPLEKQLADWYIERKKEYQVIKTEGSEIGRVNGLAVIGEQSGIVLPIEAVVAPAASKEEGKIIVTGKLGEIAKEAVQNVSAIIKRYKGEDISRYDIHVQFLQTYEGVEGDSASISVATAVISALEGIPIRQDVAMTGSLSVRGEVLPIGGATPKIEAAIEAGIKMVIIPKSNEKDVFLSKDKAEKIQIFPVETIDEVLEIALEESEKKRELLRRIRETLPLSL 635
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhh....hhhhhh..hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh......eeeeee.........eeeeee.hhhhhhhhhhhhhhhhhh.------------------------------------------------....eeee.........eee....hhhhhhhee.....----...hhhh.ee.hhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhee........hhhhhh....ee...eeeeee..hhhhhhhhhhhhhhhhhheeee...eee.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhh........ee..eeeeeeee...eeeeeeeeeeeee........eeee...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhhh..eeeee.hhhhhh..hhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1j A  18 GESLELGIEFTTTEEIEVPEKLIDQVIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVPACQGRRIVEKYREKAKSQES------------------------------------------------VLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPF----LGTPAHERVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMAKPLEKQLADWYIERKKEYQVIKTEGSEIGRVNGLAVIGEQSGIVLPIEAVVAPAASKEEGKIIVTGKLGEIAKEAVQNVSAIIKRYKGEDISRYDIHVQFLQTYEGVEGDAASISVATAVISALEGIPIRQDVAMTGSLSVRGEVLPIGGATPAIEAAIEAGIKMVIIPKSNEKDVFLSKDKAEKIQIFPVETIDEVLEIALEESEKKRELLRRIRETLPLSL 635
                                    27        37        47        57        67        77        87        97       107       117       127  |      -         -         -         -         - |     187       197       207        |-   |   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627        
                                                                                                                                          130                                              179                                  216  221                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:561
 aligned with B6YU74_THEON | B6YU74 from UniProtKB/TrEMBL  Length:635

    Alignment length:615
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629     
         B6YU74_THEON    20 SLELGIEFTTTEEIEVPEKLIDQVIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVPACQGRRIVEKYREKAKSQESVKSYILLFVMFTVMLALFIEFSATTLLMGLFVVILTIMALSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHERVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMAKPLEKQLADWYIERKKEYQVIKTEGSEIGRVNGLAVIGEQSGIVLPIEAVVAPAASKEEGKIIVTGKLGEIAKEAVQNVSAIIKRYKGEDISRYDIHVQFLQTYEGVEGDSASISVATAVISALEGIPIRQDVAMTGSLSVRGEVLPIGGATPKIEAAIEAGIKMVIIPKSNEKDVFLSKDKAEKIQIFPVETIDEVLEIALEESEKKRELLRRIRETLPLS 634
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Mg_chelatase-3k1jB03 B:39-98                                ------------------------------                                                 AAA_32-3k1jB01 B:178-414                                                                                                                                                                                                                     Lon_C-3k1jB05 B:415-616                                                                                                                                                                                   ------------------ Pfam domains (1)
           Pfam domains (2) -------------------Mg_chelatase-3k1jB04 B:39-98                                ------------------------------                                                 AAA_32-3k1jB02 B:178-414                                                                                                                                                                                                                     Lon_C-3k1jB06 B:415-616                                                                                                                                                                                   ------------------ Pfam domains (2)
         Sec.struct. author .........hhhhh....hhhhhh..hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh......eeeeee.........eeeeee.hhhhhhhhhhhhhhhh.-------------------------------------------------.....eeee.........eee....hhhhhhhee.....-----..hhhh.ee.hhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhee........hhhhhh....ee...eeeeee..hhhhhhhhhhhhhhhhhheeee...eee.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......ee..eeeeeee.....eeeeeeeeeeee.......eeeee...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhhh..eeeee.hhhhhh..hhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1j B  20 SLELGIEFTTTEEIEVPEKLIDQVIGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVPACQGRRIVEKYREKAKSQ-------------------------------------------------TVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPF-----GTPAHERVEPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKMAKPLEKQLADWYIERKKEYQVIKTEGSEIGRVNGLAVIGEQSGIVLPIEAVVAPAASKEEGKIIVTGKLGEIAKEAVQNVSAIIKRYKGEDISRYDIHVQFLQTYEGVEGDAASISVATAVISALEGIPIRQDVAMTGSLSVRGEVLPIGGATPAIEAAIEAGIKMVIIPKSNEKDVFLSKDKAEKIQIFPVETIDEVLEIALEESEKKRELLRRIRETLPLS 634
                                    29        39        49        59        69        79        89        99       109       119        |-         -         -         -         -       179       189       199       209      |  -  |    229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629     
                                                                                                                                      128                                               178                                   216   222
   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 3K1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K1J)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: S5 (103)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (B6YU74_THEON | B6YU74)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004176    ATP-dependent peptidase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        B6YU74_THEON | B6YU74: 4zpx

(-) Related Entries Specified in the PDB File

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