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(-) Description

Title :  CRYSTAL STRUCTURE OF A. FULGIDUS LON PROTEOLYTIC DOMAIN
 
Authors :  I. Botos, E. E. Melnikov, S. Cherry, S. Kozlov, O. V. Makhovskaya, J. E. Tropea, A. Gustchina, T. V. Rotanova, A. Wlodawer
Date :  01 Mar 05  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  'Atp-Dependent Protease, Catalytic Ser-Lys Dyad, B-Type Lon', Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Botos, E. E. Melnikov, S. Cherry, S. Kozlov, O. V. Makhovskaya, J. E. Tropea, A. Gustchina, T. V. Rotanova, A. Wlodawer
Atomic-Resolution Crystal Structure Of The Proteolytic Domain Of Archaeoglobus Fulgidus Lon Reveals The Conformational Variability In The Active Sites Of Lon Proteases
J. Mol. Biol. V. 351 144 2005
PubMed-ID: 16002085  |  Reference-DOI: 10.1016/J.JMB.2005.06.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PROTEASE LA HOMOLOG TYPE
    Chains: A, B, C, D, E, F
    EC Number: 3.4.21.53
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEOLYTIC DOMAIN
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Z0G)

(-) Sites  (0, 0)

(no "Site" information available for 1Z0G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z0G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys C:614 -Glu C:615

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z0G)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LON_PROTEOLYTICPS51786 Lon proteolytic domain profile.LONB_ARCFU423-602
 
 
 
 
 		  6A:423-602
B:423-602
C:423-602
D:423-602
E:423-602
F:423-602

(-) Exons   (0, 0)

(no "Exon" information available for 1Z0G)

(-) 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:195
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:198
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFK 614
               SCOP domains d1z0ga_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..eeeeeeee....eeeeeeeeeeee..---...ee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh..hhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: A:423-602 UniProt: 423-602                                                                                                                                    ------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z0g A 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFK 614
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
                                                              453 457                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:199
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
               SCOP domains d1z0gb_ B: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..eeeeeee.....eeeeeeeeeeee..---..eee....hhhhhhhhhhhhhhhhhhhhh.....eeeeeee............hhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh..hhhhh...eeeee.hhhhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: B:423-602 UniProt: 423-602                                                                                                                                    ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0g B 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
                                                              453 457                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:196
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:199
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
               SCOP domains d1z0gc_ C: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..eeeeeeee...eeeeeeeeeeeee..---...ee....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh....hhhhhheeeee.hhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: C:423-602 UniProt: 423-602                                                                                                                                    ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0g C 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
                                                              453 457                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:196
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:199
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
               SCOP domains d1z0gd_ D: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eeeeeeee....eeeeeeeeeeee..---...ee....hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee......ee....hhhhhhhhhhhhhh.eee..eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh..hhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: D:423-602 UniProt: 423-602                                                                                                                                    ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0g D 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
                                                              453 457                                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:195
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:198
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFK 614
               SCOP domains d1z0ge_ E: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..eeeeeee.....eeeeeeeeeeee..---...ee....hhhhhhhhhhhhhhhhhhh...hhh.eeeeeee............hhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh..........eeeee.hhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: E:423-602 UniProt: 423-602                                                                                                                                    ------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z0g E 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFK 614
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
                                                              453 457                                                                                                                                                             


Chain F from PDB  Type:PROTEIN  Length:196
 aligned with LONB_ARCFU | O29883 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:199
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
           LONB_ARCFU   417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSMSKSEGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
               SCOP domains d1z0gf_ F: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Lon_C-1z0gF01 F:417-602                                                                                                                                                                   ------------- Pfam domains (1)
           Pfam domains (2) Lon_C-1z0gF02 F:417-602                                                                                                                                                                   ------------- Pfam domains (2)
           Pfam domains (3) Lon_C-1z0gF03 F:417-602                                                                                                                                                                   ------------- Pfam domains (3)
           Pfam domains (4) Lon_C-1z0gF04 F:417-602                                                                                                                                                                   ------------- Pfam domains (4)
           Pfam domains (5) Lon_C-1z0gF05 F:417-602                                                                                                                                                                   ------------- Pfam domains (5)
           Pfam domains (6) Lon_C-1z0gF06 F:417-602                                                                                                                                                                   ------------- Pfam domains (6)
         Sec.struct. author .......ee..eeeeeeee...eeeeeeeeeeeee..---...ee.hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee..eee..ee.....ee...hhhhhhhhhhhhh..eeeee.hhhhhh..........eeeee.hhhhhhhhhh..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------LON_PROTEOLYTIC  PDB: F:423-602 UniProt: 423-602                                                                                                                                    ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0g F 417 KLFITEGYEVGRVNGLAVIGESAGIVLPIIAEVTPSM---EGRVIATGRLQEIAREAVMNVSAIIKKYTGRDISNMDVHIQFVGTYEGVEGDSASISIATAVISAIEGIPVDQSVAMTGSLSVKGEVLPVGGVTQKIEAAIQAGLKKVIIPKDNIDDVLLDAEHEGKIEVIPVSRINEVLEHVLEDGKKKNRLMSKFKE 615
                                   426       436       446      |  -|      466       476       486       496       506       516       526       536       546       556       566       576       586       596       606         
                                                              453 457
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z0G)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (LONB_ARCFU | O29883)
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: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: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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of 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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  Cis Peptide Bonds
    Lys C:614 - Glu C:615   [ RasMol ]  
 

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  1z0g
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  LONB_ARCFU | O29883
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  3.4.21.53
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 Related Entries

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

UniProtKB/Swiss-Prot
        LONB_ARCFU | O29883: 1z0b 1z0c 1z0e 1z0t 1z0v 1z0w

(-) Related Entries Specified in the PDB File

1z0b SAME PROTEIN E506A MUTANT
1z0c SAME PROTEIN D508A MUTANT
1z0e SAME PROTEIN MONOCLINIC FORM
1z0t SAME PROTEIN ORHORHOMBIC FORM DUAL LATTICE
1z0v SAME PROTEIN MONOCLINIC FORM DUAL LATTICE
1z0w SAME PROTEIN