1R6O - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA/ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS

Authors :   D. Xia, M. R. Maurizi, F. Guo, S. K. Singh, L. Esser

Date :   15 Oct 03 (Deposition) - 15 Feb 05 (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)
Biol. Unit 3: A,B,C,D  (1x)

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

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	CLPA, LOPD, B0882, C1019, Z1119, ECS0968
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CLPS, B0881, C1018, Z1118, ECS0967, SF0841, S0881
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 12)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	Y1	2	Ligand/Ion	YTTRIUM ION
4	YBT	4	Ligand/Ion	BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	Y1	-1	Ligand/Ion	YTTRIUM ION
4	YBT	2	Ligand/Ion	BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	Y1	-1	Ligand/Ion	YTTRIUM ION
4	YBT	2	Ligand/Ion	BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	Y1	-1	Ligand/Ion	YTTRIUM ION
4	YBT	4	Ligand/Ion	BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANEYTTRIUM
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:3 , LEU B:6 , ASN B:37 , THR B:104 , GLY B:105 , HOH B:422	BINDING SITE FOR RESIDUE CL B 144
02	AC2	SOFTWARE	HIS A:20 , HIS A:22 , GLU A:63 , HOH A:416	BINDING SITE FOR RESIDUE ZN A 411
03	AC3	SOFTWARE	HIS B:20 , HIS B:22 , GLU B:63 , HOH B:417	BINDING SITE FOR RESIDUE ZN B 412
04	AC4	SOFTWARE	HIS D:66 , HOH D:462	BINDING SITE FOR RESIDUE Y1 D 413
05	AC5	SOFTWARE	ASP D:9 , ASP D:11	BINDING SITE FOR RESIDUE Y1 D 414
06	AC6	SOFTWARE	ASN B:3 , GLN B:4 , GLU B:5 , GLU B:102 , HOH B:445 , HOH B:455 , GLU C:41	BINDING SITE FOR RESIDUE YBT B 413
07	AC7	SOFTWARE	ARG A:41 , GLU A:42 , GLU A:45 , HOH A:417	BINDING SITE FOR RESIDUE YBT A 412
08	AC8	SOFTWARE	ARG B:41 , GLU B:42 , GLU B:45 , HOH B:419 , HOH B:438 , HOH B:464 , HOH B:481	BINDING SITE FOR RESIDUE YBT B 414
09	AC9	SOFTWARE	MET A:1 , GLU A:7 , HOH A:445 , HOH A:459 , ASP C:11 , HOH C:128 , GLU D:56	BINDING SITE FOR RESIDUE YBT A 413
10	BC1	SOFTWARE	GLU A:117 , HOH C:112	BINDING SITE FOR RESIDUE GOL A 414
11	BC2	SOFTWARE	GLU B:117 , HOH B:429 , HOH B:439 , ALA D:78	BINDING SITE FOR RESIDUE GOL B 415
12	BC3	SOFTWARE	GLU B:128 , ASP B:133	BINDING SITE FOR RESIDUE GOL B 416

(no "SS Bond" information available for 1R6O)

(no "Cis Peptide Bond" information available for 1R6O)

(no "SAP(SNP)/Variant" information available for 1R6O)

(no "PROSITE Motif" information available for 1R6O)

(no "Exon" information available for 1R6O)

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 d1r6oa_ A: automated matches                                                                                                                   SCOP domains
               CATH domains 1r6oA00 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
                 1r6o 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:141
 aligned with CLPA_ECOLI | P0ABH9 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 
           CLPA_ECOLI     1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHG 141
               SCOP domains d1r6ob_ B: automated matches                                                                                                                  SCOP domains
               CATH domains 1r6oB00 B:1-141 Double Clp-N motif                                                                                                            CATH domains
           Pfam domains (1) ------------Clp_N-1r6oB01 B:13-63                              ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Clp_N-1r6oB02 B:13-63                              ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6o B   1 MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHG 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:94
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:100
                                    16        26        36        46        56        66        76        86        96       106
           CLPS_ECOLI     7 WLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d1r6oc_       C: automated matches                                                                   SCOP domains
               CATH domains 1r6oC00       C:7-106  [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
                 1r6o C   7 WLDFDQL------DALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                  |  -   |    26        36        46        56        66        76        86        96       106
                                 13     20

Chain D from PDB  Type:PROTEIN  Length:94
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:102
                                    14        24        34        44        54        64        74        84        94       104  
           CLPS_ECOLI     5 NDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d1r6od_         D: automated matches                                                                   SCOP domains
               CATH domains 1r6oD00         D:5-106  [code=3.30.1390.10, no name defined]                                          CATH domains
           Pfam domains (1) -----------------ClpS-1r6oD01 D:22-103                                                             --- Pfam domains (1)
           Pfam domains (2) -----------------ClpS-1r6oD02 D:22-103                                                             --- Pfam domains (2)
         Sec.struct. author ........--------......eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1r6o D   5 NDWLDFDQ--------ALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                   | -      | 24        34        44        54        64        74        84        94       104  
                                  12       21

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Double Clp-N motif (13)

Superfamily: Double Clp-N motif (13)

Family: Double Clp-N motif (13)

Protein domain: automated matches (3)

Escherichia coli [TaxId: 562] (3)

1a	d1r6oa_	A:
1b	d1r6ob_	B:

Class: Alpha and beta proteins (a+b) (23004)

Fold: ClpS-like (30)

Superfamily: ClpS-like (30)

Family: Adaptor protein ClpS (YljA) (17)

Protein domain: automated matches (9)

Escherichia coli [TaxId: 562] (2)

2a	d1r6oc_	C:
2b	d1r6od_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein L30; Chain: A, (164)

Homologous Superfamily: [code=3.30.1390.10, no name defined] (20)

Escherichia coli. Organism_taxid: 562. (1)

1a	1r6oC00	C:7-106
1b	1r6oD00	D:5-106

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Double Clp-N motif (16)

Homologous Superfamily: Double Clp-N motif (16)

Escherichia coli. Organism_taxid: 562. (3)

2a	1r6oB00	B:1-141
2b	1r6oA00	A:1-142

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: ClpS] (10)

Family: ClpS (10)

Escherichia coli (strain K12) (10)

1a	ClpS-1r6oD01	D:22-103
1b	ClpS-1r6oD02	D:22-103

Clan: no clan defined [family: Clp_N] (16)

Family: Clp_N (16)

Escherichia coli (strain K12) (11)

2a	Clp_N-1r6oB01	B:13-63
2b	Clp_N-1r6oB02	B:13-63

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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	1r6o
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1r6b	HIGH RESOLUTION CRYSTAL STRUCTURE OF CLPA
1r6c	HIGH RESOLUTION STRUCTURE OF CLPN
1r6q

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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Gene Ontology (13, 15)

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