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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF CLPA
 
Authors :  D. Xia, M. R. Maurizi, F. Guo, S. K. Singh, L. Esser
Date :  15 Oct 03  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  X
Keywords :  Clpa, Aaa+, N-Terminal Domain, Clps, Crystal, Binding Mechanism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Xia, L. Esser, S. K. Singh, F. Guo, M. R. Maurizi
Crystallographic Investigation Of Peptide Binding Sites In The N-Domain Of The Clpa Chaperone.
J. Struct. Biol. V. 146 166 2004
PubMed-ID: 15037248  |  Reference-DOI: 10.1016/J.JSB.2003.11.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLPA PROTEIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSK39
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR X:221 , ASP X:285 , ARG X:339 , ADP X:780BINDING SITE FOR RESIDUE MG X 782
2AC2SOFTWARELYS X:501 , THR X:502 , THR X:604 , ADP X:781BINDING SITE FOR RESIDUE MG X 783
3AC3SOFTWAREASP X:520 , SER X:522 , GLU X:565 , GLU X:639BINDING SITE FOR RESIDUE MG X 784
4AC4SOFTWAREPRO X:187 , LEU X:188 , ILE X:189 , ARG X:206 , GLY X:217 , VAL X:218 , GLY X:219 , LYS X:220 , THR X:221 , ALA X:222 , ARG X:339 , ILE X:357 , ASP X:396 , ILE X:399 , MG X:782 , HOH X:901BINDING SITE FOR RESIDUE ADP X 780
5AC5SOFTWARELEU 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 , VAL X:661 , PHE X:665 , ALA X:701 , MG X:783 , HOH X:977 , HOH X:982 , HOH X:1073BINDING SITE FOR RESIDUE ADP X 781

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R6B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu X:394 -Pro X:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R6B)

(-) 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 1R6B)

(-) 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:704
 aligned with CLPA_ECOLI | P0ABH9 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:751
                                    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 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDEPTQSSDPGSQPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGSLVDGGQVTVALDKEKNELTYGFQSAQK 751
               SCOP domains d1r6bx1 X:1-141 N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone                                                                                            d1r6bx2 X:169-436 ClpA, an Hsp100 chaperone, AAA+ modules                                                                                                                                                                                                                   d1r6bx3 X:437-751 ClpA, an Hsp100 chaperone, AAA+ modules                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1r6bX01 X:1-141 Double Clp-N motif                                                                                                                                      1r6bX02 X:169-350 P-loop containing nucleotide triphosphate hydrolases                                                                                                                1r6bX03 X:351-438  [code=1.10.8.60, no name defined]                                    1r6bX04 X:439-652 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                1r6bX05 X:653-751  [code=1.10.8.60, no name defined]                                                CATH domains
               Pfam domains ------------Clp_N-1r6bX04 X:13-63                              ------------------------------------------------------------------------------                           -----------------------------------------AAA-1r6bX01 X:210-347                                                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------AAA_2-1r6bX02 X:486-647                                                                                                                                           -----ClpB_D2-small-1r6bX03 X:653-733                                                  ------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhh.---------------------------......hhhhhhhh........hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh..hhhhh..eeee....---.......hhhhhhhhhhhhhh....eeeee..............hhhhhhhhhh........eeeeeehhhhhhh.......hhh.eeeee....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhh.eeeeee.hhh...............hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhheeee...eeee...eeeeeee.....-----------------hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhh.....eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CLPAB_1      -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CLPAB_2            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6b X   1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHG---------------------------LENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG---AGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVR-----------------AMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGSLVDGGQVTVALDKEKNELTYGFQSAQK 751
                                    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 
                                                                                                                                                                      141                         169                                                                               251 255                                                                                                                                                                                                                                                                                                                                                                610               628
   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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  1r6b
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1k6k CRYSTAL STRUCTURE OF CLPA
1ksf CRYSTAL STRUCTURE OF CLPA