3MH4 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HTRA PROTEASES ARE ACTIVATED BY A CONSERVED MECHANISM THAT CAN BE TRIGGERED BY DISTINCT MOLECULAR CUES

Authors :   T. Krojer, J. Sawa, R. Huber, T. Clausen

Date :   07 Apr 10 (Deposition) - 30 Jun 10 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (6x)
Biol. Unit 2: B  (6x)

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

Reference :   T. Krojer, J. Sawa, R. Huber, T. Clausen
Htra Proteases Have A Conserved Activation Mechanism That Can Be Triggered By Distinct Molecular Cues
Nat. Struct. Mol. Biol. V. 17 844 2010
PubMed-ID: 20581825 | Reference-DOI: 10.1038/NSMB.1840

Molecule 1 - PROTEASE DO
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DEGP
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	DEGP, HTRA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A
Biological Unit 2 (6x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3MH4)

(no "Site" information available for 3MH4)

(no "SS Bond" information available for 3MH4)

Asymmetric Unit

No.	Residues
1	Met A:42	-	Pro A:43
2	Ala A:230	-	Pro A:231
3	Met B:42	-	Pro B:43

(no "SAP(SNP)/Variant" information available for 3MH4)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	4	A:254-345 B:254-345 A:351-353 B:351-440

Biological Unit 1 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	12	A:254-345 - A:351-353 -

Biological Unit 2 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DEGP_ECOLI	280-371 377-466	12	- B:254-345 - B:351-440

(no "Exon" information available for 3MH4)

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:301
 aligned with DEGP_ECOLI | P0C0V0 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:343
                                    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   
           DEGP_ECOLI    37 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLE 379
               SCOP domains d3mh4a1 A:11-259 Protease Do (DegP                                  , HtrA), catalytic domain                                                                                                                                                            d3mh4a2 A:260-353 Protease Do (DegP, HtrA), C-terminal domains                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeeeeeeeeee.......----------------------------------.eeeeeeeeeeeeeee....eeeehhhhhh.eeeeeeee....eeeeeeeeee....eeeeeee...........hhhhh....eeeeee.......eeeeeeeeee...--------..eee...........eee.....eeeeee............eeeeehhhhhhhhhhhhhhh...............hhhhhh........ee...................ee.ee..ee...hhhhhhhh.........eeeee....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:254-345 UniProt: 280-371                                                        -----PDZ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh4 A  11 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPR----------------------------------GQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRS--------NFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLE 353
                                    20        30        40   |     -         -         -        80        90       100       110       120       130       140       150       160       170       180       | -      |200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
                                                            44                                 79                                                                                                          188      197

Chain B from PDB  Type:PROTEIN  Length:383
 aligned with DEGP_ECOLI | P0C0V0 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:436
                                    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 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLL 472
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------                                   ---------Trypsin_2-3mh4B04 B:88-224                                                                                                               ------     ---------------------------------------------------------------------------------------------------------------------------PDZ-3mh4B01      B:359-437                                                     --------- Pfam domains (1)
           Pfam domains (2) ---------------------------------                                   ---------Trypsin_2-3mh4B05 B:88-224                                                                                                               ------     ---------------------------------------------------------------------------------------------------------------------------PDZ-3mh4B02      B:359-437                                                     --------- Pfam domains (2)
           Pfam domains (3) ---------------------------------                                   -------------------------------------------------------------------------------------------------------------        -----------------------------------     ---------------------------------------------------------------------------------------------------------------------------PDZ-3mh4B03      B:359-437                                                     --------- Pfam domains (3)
         Sec.struct. author ....hhhhhhhhh..eeeeeeeeeeee......-----------------------------------.eeeeeeeeeeeeeee....eeeehhhhhh.eeeeeee.....eeeeeeeeee....eeeeeee...........hhhhh....eeeeee.......eeeeeeeeee..--------...eee...........eee.....eeeee.....-----...eeeeehhhhhhhhhhhhhhh....ee..eeee...hhhhhhh.......eeeeee...hhhhhhh.....ee.ee..ee..hhhhhhhhhhhh....eeeee......eeeee.ee...............-----.eee......eee..................eeeee..ee..hhhhhhhhh.........eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: B:254-345 UniProt: 280-371                                                        -----PDZ  PDB: B:351-440 UniProt: 377-466                                                      ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mh4 B  11 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMP-----------------------------------GQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGR--------ENFIQTDAAINRGNAGGALVNLNGELIGINTAILA-----IGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFN-----EMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLL 446
                                    20        30        40  |      -         -         -        80        90       100       110       120       130       140       150       160       170       180      |  -     | 200       210       220       230     | 240       250       260       270       280       290       300       310       320       330       340       350       360        |-    |  380       390       400       410       420       430       440      
                                                           43                                  79                                                                                                         187      196                               230   236                                                                                                                                  369   375

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 "CATH Domain" information available for 3MH4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Escherichia coli (strain K12) (21)

1a	PDZ-3mh4B01	B:359-437
1b	PDZ-3mh4B02	B:359-437
1c	PDZ-3mh4B03	B:359-437

Clan: Peptidase_PA (797)

Family: Trypsin_2 (18)

Escherichia coli (strain K12) (6)

2a	Trypsin_2-3mh4B04	B:88-224
2b	Trypsin_2-3mh4B05	B:88-224

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3mh4)

	Sites
(no "Sites" information available for 3mh4)

	Cis Peptide Bonds
		Ala A:230 - Pro A:231	[ RasMol ]
		Met A:42 - Pro A:43	[ RasMol ]
		Met B:42 - Pro B:43	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

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