2R3U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PDZ DELETION MUTANT OF DEGS

Authors :   T. Clausen, R. Kurzbauer

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

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Serine Protease, Catalytic Triad, Hydrolase, Periplasm (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	:	PET21A
	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

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2R3U)

(no "Site" information available for 2R3U)

(no "SS Bond" information available for 2R3U)

(no "Cis Peptide Bond" information available for 2R3U)

(no "SAP(SNP)/Variant" information available for 2R3U)

(no "PROSITE Motif" information available for 2R3U)

(no "Exon" information available for 2R3U)

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:202
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:210
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRD 251
               SCOP domains d2r3ua_ A: Stress sensor p    rotease DegS, catalytic domain                                                                                                                                                       SCOP domains
               CATH domains 2r3uA01 A:42-141 Trypsin-l    ike serine proteases                                                  2r3uA02 A:142-251 Trypsin-like serine proteases                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeeee.----..eeeeeeeeeeeee...eeeee........eeeee.....eee.eeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeee...........eeee...........eeee....eeeeeeee...----......eeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r3u A  42 MTPASYNLAVRRAAPAVVNVYNRGLN----NQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDK----ETPEGIGFAIPFQLATKIMDKLIRD 251
                                    51        61     |   -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|    | 231       241       251
                                                    67   72                                                                                                                                                   222  227

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:211
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDG 252
               SCOP domains d2r3ub_ B: Stress senso              r protease DegS, catalytic domain                                                                                                                                              SCOP domains
               CATH domains 2r3uB01 B:42-141 Trypsi              n-like serine proteases                                        2r3uB02 B:142-252 Trypsin-like serine proteases                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeee.--------------..eeeeee...eeeeehhhhh....eeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..............eee...........eeee....eeeee......--........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3u B  42 MTPASYNLAVRRAAPAVVNVYNR--------------LGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDK--DGETPEGIGFAIPFQLATKIMDKLIRDG 252
                                    51        61  |      -       |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|  |   231       241       251 
                                                 64             79                                                                                                                                            222  |                           
                                                                                                                                                                                                                 225

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:210
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRD 251
               SCOP domains d2r3uc_ C: Stress senso         r protease DegS, catalytic domain                                                                                                                                                  SCOP domains
               CATH domains 2r3uC01 C:42-141 Trypsi         n-like serine proteases                                             2r3uC02 C:142-251 Trypsin-like serin          e proteases                                                      CATH domains
           Pfam domains (1) --------Trypsin-2r3uC04          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (1)
           Pfam domains (2) --------Trypsin-2r3uC05          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (2)
           Pfam domains (3) --------Trypsin-2r3uC06          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhh..eeeeeee---------....eeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..----------..eee...........eeee....eeeee.....------.....eeeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r3u C  42 MTPASYNLAVRRAAPAVVNVYNR---------LEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATG----------NFLQTDASINHGNSGGALVNSLGELMGINTLSFD------TPEGIGFAIPFQLATKIMDKLIRD 251
                                    51        61  |      -  |     81        91       101       111       121       131       141       151       161       171     |   -      |191       201       211       221      |231       241       251
                                                 64        74                                                                                                    177        188                              221    228

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: 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)

1a	d2r3ua_	A:
1b	d2r3ub_	B:
1c	d2r3uc_	C:

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	2r3uB02	B:142-252
1b	2r3uC02	C:142-251
1c	2r3uA01	A:42-141
1d	2r3uC01	C:42-141
1e	2r3uB01	B:42-141
1f	2r3uA02	A:142-251

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Escherichia coli (strain K12) (21)

1a	PDZ-2r3uC01	C:248-251
1b	PDZ-2r3uC02	C:248-251
1c	PDZ-2r3uC03	C:248-251

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Escherichia coli (strain K12) (13)

2a	Trypsin-2r3uC04	C:50-245
2b	Trypsin-2r3uC05	C:50-245
2c	Trypsin-2r3uC06	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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	2r3u
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	3.4.21.-
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