2W9R - JenaLib

Title :   STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS

Authors :   V. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott, D. A. Dougan, K. Zeth

Date :   28 Jan 09 (Deposition) - 28 Apr 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Chaperone, Adaptor Protein, Dna Condensation, Iron, Clps, Clpa, Cytoplasm, N-End Rule, Dna-Binding, Iron Storage, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. J. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott, D. A. Dougan, K. Zeth
Structural Basis Of N-End Rule Substrate Recognition In Escherichia Coli By The Clpap Adaptor Protein Clps.
Embo Rep. V. 10 508 2009
PubMed-ID: 19373253 | Reference-DOI: 10.1038/EMBOR.2009.62

Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	CLPS PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH LEU-PEPTIDE
	Strain	:	K12
	Synonym	:	YLJA

Molecule 2 - DNA PROTECTION DURING STARVATION PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET
	Fragment	:	RESIDUES 10-16
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PEXB, VTM

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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 A from PDB  Type:PROTEIN  Length:97
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:97
                                                                                                                        106  
                                    21        31        41        51        61        71        81        91       101    |  
           CLPS_ECOLI    12 QLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains d2w9ra_ A: automated matches                                                                      SCOP domains
               CATH domains 2w9rA00 A:12-108  [code=3.30.1390.10, no name defined]                                            CATH domains
               Pfam domains ----------ClpS-2w9rA01 A:22-103                                                             ----- Pfam domains
         Sec.struct. author hhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 2w9r A  12 QLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    21        31        41        51        61        71        81        91       101

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with DPS_ECOLI | P0ABT2 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:11
                                    15 
            DPS_ECOLI     6 LVKSKATNLLY  16
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2w9r B   1 LVKSKATNLLY  11
                                    10

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (18, 19)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain B (DPS_ECOLI | P0ABT2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016722	oxidoreductase activity, oxidizing metal ions	Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
	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:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042594	response to starvation	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 starvation stimulus, deprivation of nourishment.
	GO:0006950	response to 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 a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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	2w9r
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	CLPS_ECOLI \| P0A8Q6
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	DPS_ECOLI \| P0ABT2
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1dps	THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DEOXYRIBONUCLEIC ACID
1f30	THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPSPROTEIN
1f33	THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPSPROTEIN
1jre	DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
1jts	DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
1l8h	DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
1l8i	DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
1lzw	STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPA SUBSTRATERECOGNITION
1mbu	CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER
1mbv	CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER TETRAGONALFORM
1mbx	CRYSTAL STRUCTURE ANALYSIS OF CLPSN WITH TRANSITION METALION BOUND
1mg9	THE STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPASUBSTRATE RECOGNITION
1r6o	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA/ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS
1r6q	CLPNS WITH FRAGMENTS

Description