2R3Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DEGS PROTEASE IN COMPLEX WITH THE YWF ACTIVATING PEPTIDE

Authors :   T. Clausen, H. Hasselblatt

Date :   30 Aug 07 (Deposition) - 27 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Reversible Activation Of A Protease, Catalytic Triad, Hydrolase, Periplasm, Serine Protease, Hydrolase/Hydrolase Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Hasselblatt, R. Kurzbauer, C. Wilken, T. Krojer, J. Sawa, J. Kurt, R. Kirk, S. Hasenbein, M. Ehrmann, T. Clausen
Regulation Of The Sigmae Stress Response By Degs: How The Pdz Domain Keeps The Protease Inactive In The Resting State And Allows Integration Of Different Omp-Derived Stress Signals Upon Folding Stress.
Genes Dev. V. 21 2659 2007
PubMed-ID: 17938245 | Reference-DOI: 10.1101/GAD.445307
(for further references see the PDB file header)

Molecule 1 - PROTEASE DEGS
	Chains	:	A, B, C
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15-B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DEGS, HHOB, HTRH
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - SYNTHETIC PEPTIDE YWF
	Chains	:	D, E, F
	Engineered	:	YES
	Other Details	:	THE YWF PEPTIDE MIMICS THE C-TERMINUS OF OUTER MEMBRANE PROTEINS.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2R3Y)

(no "Site" information available for 2R3Y)

(no "SS Bond" information available for 2R3Y)

(no "Cis Peptide Bond" information available for 2R3Y)

(no "SAP(SNP)/Variant" information available for 2R3Y)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGS_ECOLI	281-326	3	A:282-326 B:282-326 C:282-326

(no "Exon" information available for 2R3Y)

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:280
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:311
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAANAGIQVNDLIISVDNKPAISALETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQEYP 352
               SCOP domains -d2r3ya2 A:43-254 Stress sensor protease DegS, catalytic domain                                                                                                                                                      d2r3ya1 A                  :255-352 Stress sensor protease      DegS, C-terminal         domain    SCOP domains
               CATH domains 2r3yA01 A:42-145,A:238-254 Trypsin-like serine proteases                                                2r3yA02 A:146-237 Trypsin-like serine proteases                                             2r3yA01          -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeee.........eeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eeee....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee..ee.------------------.........hhhhh.................-----hhhhhh......ee....--------..ee.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:282-326 UniProt: 281-326          -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3y A  42 MTPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGG------------------IVVNEVSPDGPAANAGIQVNDLIISVDNKPA-----TMDQVAEIRPGSVIPVVV--------LQVTIQEYP 352
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 |       -         -|      291       301       311|     |321       331   |     -  |    351 
                                                                                                                                                                                                                                                       263                282                           312   318              335      344

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:311
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAANAGIQVNDLIISVDNKPAISALETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQEYP 352
               SCOP domains -d2r3yb2 B:43-254 Stress       sensor protease DegS, catalytic domain                                                                                                                                                d2r3yb1 B                  :255-352 Stress sensor protease      DegS, C-terminal         domain    SCOP domains
               CATH domains 2r3yB01 B:42-145,B:238-25      4 Trypsin-like serine proteases                                          2r3yB02 B:146-237 Trypsin-like serine proteases                                             2r3yB01          ---------                  -------------------------------     ------------------        --------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeee.------..eeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eeee....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee.....------------------..........hhhhh................-----hhhhhhh.....ee....--------..ee.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: B:282-326 UniProt: 281-326          -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3y B  42 MTPASYNLAVRRAAPAVVNVYNRGL------QLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGG------------------IVVNEVSPDGPAANAGIQVNDLIISVDNKPA-----TMDQVAEIRPGSVIPVVV--------LQVTIQEYP 352
                                    51        61    |    - |      81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 |       -         -|      291       301       311|     |321       331   |     -  |    351 
                                                   66     73                                                                                                                                                                                           263                282                           312   318              335      344

Chain C from PDB  Type:PROTEIN  Length:275
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:311
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAANAGIQVNDLIISVDNKPAISALETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQEYP 352
               SCOP domains -d2r3yc2 C:43-254 Stress s     ensor protease DegS, catalytic domain                                                                                                                                                 d2r3yc1 C                  :255-352 Stress sensor protease      DegS, C-terminal         domain    SCOP domains
               CATH domains 2r3yC01 C:42-145,C:238-254      Trypsin-like serine proteases                                           2r3yC02 C:146-237 Trypsin-like serine proteases                                             2r3yC01          ---------                  -------------------------------     ------------------        --------- CATH domains
           Pfam domains (1) --------Trypsin-2r3yC04 C:     50-245                                                                                                                                                                       --PDZ-2r3yC01 C:24                  8-335                                                         --------- Pfam domains (1)
           Pfam domains (2) --------Trypsin-2r3yC05 C:     50-245                                                                                                                                                                       --PDZ-2r3yC02 C:24                  8-335                                                         --------- Pfam domains (2)
           Pfam domains (3) --------Trypsin-2r3yC06 C:     50-245                                                                                                                                                                       --PDZ-2r3yC03 C:24                  8-335                                                         --------- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhh..eeeeeeee..-----..eeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eeee....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee..ee.------------------.........hhhhh.................-----hhhhhhh.....ee....--------..ee.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: C:282-326 UniProt: 281-326          -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3y C  42 MTPASYNLAVRRAAPAVVNVYNRGLN-----QLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIGG------------------IVVNEVSPDGPAANAGIQVNDLIISVDNKPA-----TMDQVAEIRPGSVIPVVV--------LQVTIQEYP 352
                                    51        61     |   - |      81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 |       -         -|      291       301       311|     |321       331   |     -  |    351 
                                                    67    73                                                                                                                                                                                           263                282                           312   318              335      344

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author ..ee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2r3y D 407 VYWF 410

Chain E from PDB  Type:PROTEIN  Length:4
                                    
               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
                 2r3y E 407 VYWF 410

Chain F from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author ..ee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2r3y F 407 VYWF 410

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: HtrA-like serine proteases (12)

Protein domain: Stress sensor protease DegS, C-terminal domain (5)

Escherichia coli [TaxId: 562] (5)

1a	d2r3ya1	A:255-352
1b	d2r3yb1	B:255-352
1c	d2r3yc1	C:255-352

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Prokaryotic proteases (131)

Protein domain: Stress sensor protease DegS, catalytic domain (11)

Escherichia coli [TaxId: 562] (11)

2a	d2r3ya2	A:43-254
2b	d2r3yb2	B:43-254
2c	d2r3yc2	C:43-254

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Escherichia coli. Organism_taxid: 562. (11)

1a	2r3yA02	A:146-237
1b	2r3yB02	B:146-237
1c	2r3yC02	C:146-237
1d	2r3yB01	B:42-145,B:238-254
1e	2r3yC01	C:42-145,C:238-254
1f	2r3yA01	A:42-145,A:238-254

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Escherichia coli (strain K12) (21)

1a	PDZ-2r3yC01	C:248-335
1b	PDZ-2r3yC02	C:248-335
1c	PDZ-2r3yC03	C:248-335

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Escherichia coli (strain K12) (13)

2a	Trypsin-2r3yC04	C:50-245
2b	Trypsin-2r3yC05	C:50-245
2c	Trypsin-2r3yC06	C:50-245

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DEGS_ECOLI | P0AEE3)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0071218	cellular response to misfolded protein	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a misfolded protein stimulus.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0071575	integral component of external side of plasma membrane	The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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(no "Sites" information available for 2r3y)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r3y)

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	2r3y
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	3.4.21.-
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1sot	DEGS
1soz	DEGS/YQF
1vcw	DEGS BACKSOAK
2r3u	DEGS DELTA PDZ

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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SCOP Domains (2, 6)

CATH Domains (1, 6)

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