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(-) Description

Title :  CRYSTAL STRUCTURE OF HSLV FROM THERMOTOGA MARITIMA
 
Authors :  H. K. Song, R. Ramachandran, M. B. Bochtler, C. Hartmann, M. K. Azim, R. H
Date :  05 Jul 02  (Deposition) - 06 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (4x)
Keywords :  N-Terminal Catalytic Threonine Residue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. K. Song, M. Bochtler, M. K. Azim, C. Hartmann, R. Huber, R. Ramachandran
Isolation And Characterization Of The Prokaryotic Proteasom Homolog Hslvu (Clpqy) From Thermotoga Maritima And The Crystal Structure Of Hslv.
Biophys. Chem. V. 100 437 2003
PubMed-ID: 12646382  |  Reference-DOI: 10.1016/S0301-4622(02)00297-1

(-) Compounds

Molecule 1 - ATP-DEPENDENT PROTEASE HSLV
    ChainsA, B, C
    EC Number3.4.25.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTHREE PROTOMERS
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (4x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:156 , CYS C:159 , THR C:162 , HOH C:268 , HOH C:288 , HOH C:301BINDING SITE FOR RESIDUE NA C 250
2AC2SOFTWAREGLY B:156 , CYS B:159 , THR B:162 , HOH B:253 , HOH B:271 , HOH B:290BINDING SITE FOR RESIDUE NA B 251
3AC3SOFTWAREGLY A:156 , CYS A:159 , THR A:162 , HOH A:257 , HOH A:273 , HOH A:294BINDING SITE FOR RESIDUE NA A 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M4Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1M4Y)

(-) 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:171
 aligned with HSLV_THEMA | Q9WYZ1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 
           HSLV_THEMA     6 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 176
               SCOP domains d1m4ya_ A: HslV (ClpQ) protease                                                                                                                                             SCOP domains
               CATH domains 1m4yA00 A:1-171 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee...eee..eeee.....eeee....eeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh..eeeee....eeee.....ee.....eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4y A   1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with HSLV_THEMA | Q9WYZ1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 
           HSLV_THEMA     6 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 176
               SCOP domains d1m4yb_ B: HslV (ClpQ) protease                                                                                                                                             SCOP domains
               CATH domains 1m4yB00 B:1-171 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee...eee..eeee.....eeee....eeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.eeeeee....eeeee....ee.....eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4y B   1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

Chain C from PDB  Type:PROTEIN  Length:171
 aligned with HSLV_THEMA | Q9WYZ1 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 
           HSLV_THEMA     6 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 176
               SCOP domains d1m4yc_ C: HslV (ClpQ) protease                                                                                                                                             SCOP domains
               CATH domains 1m4yC00 C:1-171 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                                                                  CATH domains
           Pfam domains (1) Proteasome-1m4yC01 C:1-171                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) Proteasome-1m4yC02 C:1-171                                                                                                                                                  Pfam domains (2)
           Pfam domains (3) Proteasome-1m4yC03 C:1-171                                                                                                                                                  Pfam domains (3)
         Sec.struct. author ..eeeeee..eeeeee...eee..eeee.....eeee....eeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh..eeeee....eeee.....ee.....eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m4y C   1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWRTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTIAGEICIYTNQNIVIEEV 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (HSLV_THEMA | Q9WYZ1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004298    threonine-type endopeptidase activity    Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism in which the hydroxyl group of a threonine residue at the active center acts as a nucleophile.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
cellular component
    GO:0009376    HslUV protease complex    A protein complex that possesses ATP-dependent protease activity; consists of an ATPase large subunit with homology to other ClpX family ATPases and a peptidase small subunit related to the proteasomal beta-subunits of eukaryotes. In the E. coli complex, a double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005839    proteasome core complex    A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.

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1ned CRYSTAL STRUCTURE OF HSLV FROM E. COLI