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(-) Description

Title :  CRYSTAL STRUCTURE OF CLPA, AN HSP100 CHAPERONE AND REGULATOR OF CLPAP PROTEASE: STRUCTURAL BASIS OF DIFFERENCES IN FUNCTION OF THE TWO AAA+ ATPASE DOMAINS
 
Authors :  F. Guo, M. R. Maurizi, L. Esser, D. Xia
Date :  12 Jan 02  (Deposition) - 27 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  X
Keywords :  Clpa, Aaa+, Atpases, Atp-Dependent Protease, Chaperones, Crystal Structure, Hydrolase, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Guo, M. R. Maurizi, L. Esser, D. Xia
Crystal Structure Of Clpa, An Hsp100 Chaperone And Regulator Of Clpap Protease
J. Biol. Chem. V. 277 46743 2002
PubMed-ID: 12205096  |  Reference-DOI: 10.1074/JBC.M207796200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ENDOPEPTIDASE CLP ATP-BINDING

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2IPA5Ligand/IonISOPROPYL ALCOHOL
3MET1Mod. Amino AcidMETHIONINE
4MG2Ligand/IonMAGNESIUM ION
5PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS X:501 , ADP X:781BINDING SITE FOR RESIDUE MG X 782
02AC2SOFTWAREASP X:520 , SER X:522 , GLU X:565 , GLU X:639BINDING SITE FOR RESIDUE MG X 783
03AC3SOFTWAREARG X:90 , HIS X:94 , ASN X:107 , VAL X:110 , ALA X:111 , ILE X:138 , ASP X:674 , HOH X:908BINDING SITE FOR RESIDUE PGE X 785
04AC4SOFTWARELYS X:387 , TYR X:388 , ALA X:434 , ARG X:435 , GLU X:484BINDING SITE FOR RESIDUE PGE X 786
05AC5SOFTWAREPRO X:187 , LEU X:188 , ILE X:189 , ARG X:206 , GLU X:215 , GLY X:217 , GLY X:219 , LYS X:220 , THR X:221 , ALA X:222 , ARG X:339 , ASP X:396 , ILE X:399 , HOH X:901BINDING SITE FOR RESIDUE ADP X 780
06AC6SOFTWARELEU X:459 , VAL X:460 , PHE X:461 , GLN X:463 , GLY X:498 , VAL X:499 , GLY X:500 , LYS X:501 , THR X:502 , GLU X:503 , LEU X:653 , VAL X:661 , PHE X:665 , ALA X:701 , MG X:782 , HOH X:977 , HOH X:982 , HOH X:1073BINDING SITE FOR RESIDUE ADP X 781
07AC7SOFTWAREGLU X:523 , THR X:637BINDING SITE FOR RESIDUE IPA X 791
08AC8SOFTWAREGLN X:89 , PHE X:93 , ASP X:663BINDING SITE FOR RESIDUE IPA X 792
09AC9SOFTWARESER X:97 , ARG X:435 , GLN X:672 , GLN X:675BINDING SITE FOR RESIDUE IPA X 794
10BC1SOFTWAREGLU X:102 , GLU X:427 , HOH X:968BINDING SITE FOR RESIDUE IPA X 795
11BC2SOFTWAREPRO X:349 , LEU X:394 , HOH X:891BINDING SITE FOR RESIDUE IPA X 796

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLPAB_1PS00870 Chaperonins clpA/B signature 1.CLPA_ECOLI302-314  1X:302-314
2CLPAB_2PS00871 Chaperonins clpA/B signature 2.CLPA_ECOLI518-536  1X:518-536

(-) Exons   (0, 0)

(no "Exon" information available for 1KSF)

(-) 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:715
 aligned with CLPA_ECOLI | P0ABH9 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:757
                                    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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       
           CLPA_ECOLI     1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDEPTQSSDPGSQPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGSLVDGGQVTVALDKEKNELTYGFQSAQKHKAEAA 757
               SCOP domains d1ksfx1 X:1-142 N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone                                                                                           d1ksfx2 X:168-436 ClpA, an Hsp100 chaperone, AAA+ modules                                                                                                                                                                                                                    d1ksfx3 X:437-755 ClpA, an Hsp100 chaperone, AAA+ modules                                                                                                                                                                                                                                                                       - SCOP domains
               CATH domains 1ksfX01 X:1-142 Double Clp-N motif                                                                                                                                     1ksfX02 X:168-350 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 1ksfX03 X:351-438  [code=1.10.8.60, no name defined]                                    1ksfX04 X:439-652 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                1ksfX05 X:653-754  [code=1.10.8.60, no name defined]                                                  - - CATH domains
               Pfam domains ------------Clp_N-1ksfX04 X:13-63                              -------------------------------------------------------------------------------                         ------------------------------------------AAA-1ksfX01 X:210-347                                                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------AAA_2-1ksfX02 X:486-647                                                                                                                                           -----ClpB_D2-small-1ksfX03 X:653-733                                                  ---------------------- - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eehhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhh..-------------------------.......hhhhhhhh........hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh..........eeee....---.......hhhhhhhhhhhhh.....eeeee..............hhhhhhh...........eeeeeehhhhhhh.......hhh.eeeee....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhh.eeeeee.hhh...............hhhhhh.hhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhee.......ee...eeeeeee.....-------------.....hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhh.....eeeeeeee....eeeeeeee.......-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CLPAB_1      -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CLPAB_2            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ksf X   1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT-------------------------RLENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG---AGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVR-------------NSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGSLVDGGQVTVALDKEKNELTYGFQSAQKHKAE-M 784
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |       -         -       170       180       190       200       210       220       230       240       250|   |  260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610         -   |   630       640       650       660       670       680       690       700       710       720       730       740       750    | |
                                                                                                                                                                       142                       168                                                                                251 255                                                                                                                                                                                                                                                                                                                                                                610           624                                                                                                                                755 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              784
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: ClpB_D2-small] (9)
(-)
Clan: no clan defined [family: Clp_N] (16)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (CLPA_ECOLI | P0ABH9)
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:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    GO:0043335    protein unfolding    The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    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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  1ksf
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  CLPA_ECOLI | P0ABH9
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPA_ECOLI | P0ABH9: 1k6k 1lzw 1mbu 1mbv 1mbx 1mg9 1r6b 1r6c 1r6o 1r6q

(-) Related Entries Specified in the PDB File

1k6k