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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF CLPSN WITH TRANSITION METAL ION BOUND
 
Authors :  F. Guo, L. Esser, S. K. Singh, M. R. Maurizi, D. Xia
Date :  03 Aug 02  (Deposition) - 11 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein Binding, Adaptors, Hsp100/Clp Chaperone, Aaa+ Family, Atp- Dependent Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Guo, L. Esser, S. K. Singh, M. R. Maurizi, D. Xia
Crystal Structure Of The Heterodimeric Complex Of The Adaptor, Clps, With The N-Domain Of The Aaa+ Chaperone, Clp
J. Biol. Chem. V. 277 46753 2002
PubMed-ID: 12235156  |  Reference-DOI: 10.1074/JBC.M208104200

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLP A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD33-YLJA
    Expression System Strain: DH5 ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - PROTEIN YLJA
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFG42
    Expression System Strain: SG22176
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3YBT5Ligand/IonBIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3YBT2Ligand/IonBIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3YBT3Ligand/IonBIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
4ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:3 , LEU B:6 , ASN B:37 , THR B:104 , GLY B:105BINDING SITE FOR RESIDUE CL B 143
02AC2SOFTWAREHIS A:20 , HIS A:22 , GLU A:63 , HOH A:214BINDING SITE FOR RESIDUE ZN A 210
03AC3SOFTWAREHIS B:20 , HIS B:22 , GLU B:63 , HOH B:216BINDING SITE FOR RESIDUE ZN B 211
04AC4SOFTWAREASN B:3 , GLN B:4 , GLU B:5 , GLU B:102 , HOH B:250 , HOH B:262 , GLU C:41BINDING SITE FOR RESIDUE YBT B 212
05AC5SOFTWAREARG A:41 , GLU A:42 , GLU A:45 , HOH A:215 , HOH A:253BINDING SITE FOR RESIDUE YBT A 211
06AC6SOFTWAREARG B:41 , GLU B:42 , GLU B:45 , HOH B:218 , HOH B:241 , HOH B:272BINDING SITE FOR RESIDUE YBT B 213
07AC7SOFTWAREMET A:1 , GLU A:7 , ASP D:54 , GLU D:56 , HOH D:140BINDING SITE FOR RESIDUE YBT A 212
08AC8SOFTWAREGLU A:19 , ASN D:34 , ASP D:35 , ASP D:36 , TYR D:37 , THR D:38 , MET D:40 , MET D:62 , HIS D:66BINDING SITE FOR RESIDUE YBT D 107
09AC9SOFTWAREGLU A:117 , HOH A:260 , HOH C:113BINDING SITE FOR RESIDUE GOL A 213
10BC1SOFTWAREGLU B:117 , HOH B:231 , HOH B:242BINDING SITE FOR RESIDUE GOL B 214
11BC2SOFTWAREGLU B:128 , ASP B:133BINDING SITE FOR RESIDUE GOL B 215

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MBX)

(-) 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:142
 aligned with CLPA_ECOLI | P0ABH9 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
           CLPA_ECOLI     1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT 142
               SCOP domains d1mbxa_ A: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone                                                                        SCOP domains
               CATH domains 1mbxA00 A:1-142 Double Clp-N motif                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mbx A   1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with CLPA_ECOLI | P0ABH9 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
           CLPA_ECOLI     1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT 142
               SCOP domains d1mbxb_ B: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone                                                                        SCOP domains
               CATH domains 1mbxB00 B:1-142 Double Clp-N motif                                                                                                             CATH domains
           Pfam domains (1) ------------Clp_N-1mbxB01 B:13-63                              ------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------Clp_N-1mbxB02 B:13-63                              ------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mbx B   1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain C from PDB  Type:PROTEIN  Length:87
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:87
                                    29        39        49        59        69        79        89        99       
           CLPS_ECOLI    20 DALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d1mbxc_ C: Adaptor protein ClpS (YljA)                                                  SCOP domains
               CATH domains 1mbxC00 C:20-106  [code=3.30.1390.10, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1mbx C  20 DALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    29        39        49        59        69        79        89        99       


Chain D from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                    30        40        50        60        70        80        90       100      
           CLPS_ECOLI    21 ALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d1mbxd_ D: Adaptor protein ClpS (YljA)                                                 SCOP domains
               CATH domains 1mbxD00 D:21-106  [code=3.30.1390.10, no name defined]                                 CATH domains
           Pfam domains (1) -ClpS-1mbxD01 D:22-103                                                             --- Pfam domains (1)
           Pfam domains (2) -ClpS-1mbxD02 D:22-103                                                             --- Pfam domains (2)
         Sec.struct. author ......eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1mbx D  21 ALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    30        40        50        60        70        80        90       100
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: ClpS] (10)
(-)
Clan: no clan defined [family: Clp_N] (16)

(-) Gene Ontology  (13, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D   (CLPS_ECOLI | P0A8Q6)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    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: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:0009408    response to heat    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 a heat stimulus, a temperature stimulus above the optimal temperature for that organism.

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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 1mg9 1r6b 1r6c 1r6o 1r6q
        CLPS_ECOLI | P0A8Q6: 1lzw 1mbu 1mbv 1mg9 1r6o 1r6q 2w9r 2wa8 2wa9 3o1f 3o2b 3o2h 3o2o

(-) Related Entries Specified in the PDB File

1mbu CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER
1mbv CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER TETERAGONAL FORM