3OU0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   RE-REFINED 3CS0

Authors :   R. T. Sauer, R. A. Grant, S. Kim

Date :   14 Sep 10 (Deposition) - 19 Jan 11 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (24x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kim, R. A. Grant, R. T. Sauer
Covalent Linkage Of Distinct Substrate Degrons Controls Assembly And Disassembly Of Degp Proteolytic Cages.
Cell(Cambridge, Mass. ) V. 145 67 2011
PubMed-ID: 21458668 | Reference-DOI: 10.1016/J.CELL.2011.02.024

Molecule 1 - PERIPLASMIC SERINE ENDOPROTEASE DEGP
	Chains	:	A
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	DEGP, UNP RESIDUES 27-474
	Gene	:	B0161, DEGP, HTRA, JW0157, PTD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PROTEASE DO, DEGP

Molecule 2 - PENTAPEPTIDE
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - HEPTAPEPTIDE
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (24x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 25)

No.	Name	Count	Type	Full Name
1	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
2	UNK	12	Mod. Amino Acid

Biological Unit 1 (1, 312)

No.	Name	Count	Type	Full Name
1	MSE	312	Mod. Amino Acid	SELENOMETHIONINE
2	UNK	-1	Mod. Amino Acid

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MSE	-1	Mod. Amino Acid	SELENOMETHIONINE
2	UNK	-1	Mod. Amino Acid

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MSE	-1	Mod. Amino Acid	SELENOMETHIONINE
2	UNK	-1	Mod. Amino Acid

(no "Site" information available for 3OU0)

(no "SS Bond" information available for 3OU0)

(no "Cis Peptide Bond" information available for 3OU0)

(no "SAP(SNP)/Variant" information available for 3OU0)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	2	A:254-345 A:351-440

Biological Unit 1 (1, 48)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	48	A:254-345 A:351-440

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	0	- -

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	0	- -

(no "Exon" information available for 3OU0)

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:392
 aligned with DEGP_ECOLI | P0C0V0 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:438
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466        
           DEGP_ECOLI    37 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ 474
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------Trypsin_2-3ou0A03 A:88-224                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------PDZ-3ou0A01 A:359-437                                                          ----------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ-3ou0A02 A:359-437                                                          ----------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhh..eeeeeeee..----------------------------------------------..eeeeeeeeeee....eeeeehhhhh.eeeeeee.....eeeeeeeeee....eeeeee............hhhhh....eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eee.....eeeeeeeee.........eeeeehhhhhhhhhhhhhhh........eeeee.hhhhhhhh.......eeeeee...hhhhhhh.....eeeee..ee..hhhhhhhhhh......eeeeeeee..eeeeeeee........eehhhhhh....eeeee......eeeeee...............eeeee..ee..hhhhhhhhhh.....eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:254-345 UniProt: 280-371                                                        -----PDZ  PDB: A:351-440 UniProt: 377-466                                                      -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ou0 A  11 QmPSLAPmLEKVmPSVVSINVEGST----------------------------------------------QKFmALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKmVGKDPRSDIALIQIQNPKNLTAIKmADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNmVKNLTSQmVEYGQVKRGELGImGTELNSELAKAmKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTmPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEmSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLmQ 448
                             |     |20  |     30    |    -         -         -         -         - |  |   90       100       110       120      |130       140       150 |     160       170       180       190       200       210       220       230       240     | 250   |   260       270       280       290       300       310       320       330|      340       350       360       370     | 380       390       400       410       420       430       440      | 
                             |     |    |          35                                             82  |                                       127-MSE                  152-MSE                                                                                       246-MSE 254-MSE       268-MSE     280-MSE                                            331-MSE                                      376-MSE                                                                447-MSE
                            12-MSE |    |                                                            85-MSE                                                                                                                                                                                                                                                                                                                                                                       
                                  18-MSE|                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                       23-MSE

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .eee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3ou0 B 371 xxxxx 375
                            |||||
                            |||||
                          371-UNK
                           372-UNK
                            373-UNK
                             374-UNK
                              375-UNK

Chain C from PDB  Type:PROTEIN  Length:7
                                       
               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
                 3ou0 C 501 xxxxxxx 507
                            |||||||
                            |||||||
                          501-UNK||
                           502-UNK|
                            503-UNK
                             504-UNK
                              505-UNK
                               506-UNK
                                507-UNK

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 '\|'

(no "SCOP Domain" information available for 3OU0)

(no "CATH Domain" information available for 3OU0)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Escherichia coli (strain K12) (21)

1a	PDZ-3ou0A01	A:359-437
1b	PDZ-3ou0A02	A:359-437

Clan: Peptidase_PA (797)

Family: Trypsin_2 (18)

Escherichia coli (strain K12) (6)

Trypsin_2-3ou0A03

A:88-224

Asymmetric Unit(hide GO term definitions)

Chain A (DEGP_ECOLI | P0C0V0)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0006515	misfolded or incompletely synthesized protein catabolic process	The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	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.
	GO:0009266	response to temperature stimulus	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 temperature stimulus.
cellular component
	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.

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Biological Units
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	3ou0
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	3.4.21.-
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	DEGP_ECOLI \| P0C0V0	:	1ky9 2zle 3cs0 3mh4 3mh5 3mh6 3mh7 3otp 4a8d

3cs0	CRYSTAL STRUCTURE OF DEGP24. THIS ENTRY 3OU0 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3CS0SF
3otp	CRYSTAL STRUCTURE OF THE DEGP DODECAMER WITH A MODEL SUBSTRATE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 25)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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