1I78 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHIA COLI

Authors :   L. Vandeputte-Rutten, R. A. Kramer, J. Kroon, N. Dekker, M. R. Egmond, P

Date :   08 Mar 01 (Deposition) - 03 Oct 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: A (1x),B (1x)

Keywords :   Integral Outer Membrane Protein, Protease, Beta Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Vandeputte-Rutten, R. A. Kramer, J. Kroon, N. Dekker, M. R. Egmond, P. Gros
Crystal Structure Of The Outer Membrane Protease Ompt From Escherichia Coli Suggests A Novel Catalytic Site.
Embo J. V. 20 5033 2001
PubMed-ID: 11566868 | Reference-DOI: 10.1093/EMBOJ/20.18.5033

Molecule 1 - PROTEASE VII
	Chains	:	A, B
	EC Number	:	3.4.21.87
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRAK11
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	OMPT
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	OMPT, OMPTIN, OUTER MEMBRANE PROTEIN 3B

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BOG	4	Ligand/Ion	B-OCTYLGLUCOSIDE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	BOG	4	Ligand/Ion	B-OCTYLGLUCOSIDE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE B:52 , GLY B:70 , TRP B:71 , THR B:72 , ASN B:110	BINDING SITE FOR RESIDUE BOG B 600
2	AC2	SOFTWARE	LYS A:53 , GLY A:54 , GLY A:70 , THR A:72 , TYR A:108 , ASN A:110 , PHE A:112 , ARG A:138	BINDING SITE FOR RESIDUE BOG A 700
3	AC3	SOFTWARE	ALA A:237 , TYR A:248 , VAL A:249 , TYR B:134 , LYS B:177 , PRO B:179	BINDING SITE FOR RESIDUE BOG B 800
4	AC4	SOFTWARE	ALA A:69 , GLY A:75 , SER A:76 , PHE A:112	BINDING SITE FOR RESIDUE BOG A 900
5	AC5	SOFTWARE	THR A:2 , GLN A:63 , TRP A:119 , LEU B:18 , GLY B:19 , THR B:20 , THR B:289	BINDING SITE FOR RESIDUE MPD A 710
6	AC6	SOFTWARE	LEU A:5 , VAL B:249 , THR B:289	BINDING SITE FOR RESIDUE MPD A 720

(no "SS Bond" information available for 1I78)

(no "Cis Peptide Bond" information available for 1I78)

(no "SAP(SNP)/Variant" information available for 1I78)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPTIN_1	PS00834	Aspartyl proteases, omptin family signature 1.	OMPT_ECOLI	115-124	2	A:95-104 B:95-104
2	OMPTIN_2	PS00835	Aspartyl proteases, omptin family signature 2.	OMPT_ECOLI	152-168	2	A:132-148 B:132-148

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPTIN_1	PS00834	Aspartyl proteases, omptin family signature 1.	OMPT_ECOLI	115-124	1	A:95-104 -
2	OMPTIN_2	PS00835	Aspartyl proteases, omptin family signature 2.	OMPT_ECOLI	152-168	1	A:132-148 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPTIN_1	PS00834	Aspartyl proteases, omptin family signature 1.	OMPT_ECOLI	115-124	1	- B:95-104
2	OMPTIN_2	PS00835	Aspartyl proteases, omptin family signature 2.	OMPT_ECOLI	152-168	1	- B:132-148

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPTIN_1	PS00834	Aspartyl proteases, omptin family signature 1.	OMPT_ECOLI	115-124	2	A:95-104 B:95-104
2	OMPTIN_2	PS00835	Aspartyl proteases, omptin family signature 2.	OMPT_ECOLI	152-168	2	A:132-148 B:132-148

Biological Unit 4 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OMPTIN_1	PS00834	Aspartyl proteases, omptin family signature 1.	OMPT_ECOLI	115-124	2	A:95-104 B:95-104
2	OMPTIN_2	PS00835	Aspartyl proteases, omptin family signature 2.	OMPT_ECOLI	152-168	2	A:132-148 B:132-148

(no "Exon" information available for 1I78)

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:297
 aligned with OMPT_ECOLI | P09169 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:297
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
           OMPT_ECOLI    21 STETLSFTPDNINADISLGTLSGKTKERVYLAEEGGRKVSQLDWKFNNAAIIKGAINWDLMPQISIGAAGWTTLGSRGGNMVDQDWMDSSNPGTWTDESRHPDTQLNYANEFDLNIKGWLLNEPNYRLGLMAGYQESRYSFTARGGSYIYSSEEGFRDDIGSFPNGERAIGYKQRFKMPYIGLTGSYRYEDFELGGTFKYSGWVESSDNDEHYDPGKRITYRSKVKDQNYYSVAVNAGYYVTPNAKVYVEGAWNRVTNKKGNTSLYDHNNNTSDYSKNGAGIENYNFITTAGLKYTF 317
               SCOP domains d1i78a_ A: Outer membrane protease OMPT                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1i78A00 A:1-297 OMPT-like                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeee.....eeeeeeeeee...eeeeeeeee...........eeeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee..eee...................eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------OMPTIN_1  ---------------------------OMPTIN_2         ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i78 A   1 STETLSFTPDNINADISLGTLSGKTKERVYLAEEGGRKVSQLDWKFNNAAIIKGAINWDLMPQISIGAAGWTTLGSRGGNMVDQDWMDSSNPGTWTDEARHPDTQLNYANEFDLNIKGWLLNEPNYRLGLMAGYQESRYSFTARGGSYIYSSEEGFRDDIGSFPNGERAIGYKQRFKMPYIGLTGSYRYEDFELGGTFKYSGWVESSDNDEHYDPKGRITYRSKVKDQNYYSVAVNAGYYVTPNAKVYVEGAWNRVTNKKGNTSLYDHNNNTSDYSKNGAGIENYNFITTAGLKYTF 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with OMPT_ECOLI | P09169 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:287
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
           OMPT_ECOLI    31 NINADISLGTLSGKTKERVYLAEEGGRKVSQLDWKFNNAAIIKGAINWDLMPQISIGAAGWTTLGSRGGNMVDQDWMDSSNPGTWTDESRHPDTQLNYANEFDLNIKGWLLNEPNYRLGLMAGYQESRYSFTARGGSYIYSSEEGFRDDIGSFPNGERAIGYKQRFKMPYIGLTGSYRYEDFELGGTFKYSGWVESSDNDEHYDPGKRITYRSKVKDQNYYSVAVNAGYYVTPNAKVYVEGAWNRVTNKKGNTSLYDHNNNTSDYSKNGAGIENYNFITTAGLKYTF 317
               SCOP domains d1i78b_ B: Outer membrane protease OMPT                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1i78B00 B:11-297 OMPT-like                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.hhhh..eeeeeeeeeeeeeeeeeeeeee....eeeeeeeeee...eeeeeeeee...........eeee...eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee...eeee........eeee.......eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeee.hhhhheeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------OMPTIN_1  ---------------------------OMPTIN_2         ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i78 B  11 NINADISLGTLSGKTKERVYLAEEGGRKVSQLDWKFNNAAIIKGAINWDLMPQISIGAAGWTTLGSRGGNMVDQDWMDSSNPGTWTDEARHPDTQLNYANEFDLNIKGWLLNEPNYRLGLMAGYQESRYSFTARGGSYIYSSEEGFRDDIGSFPNGERAIGYKQRFKMPYIGLTGSYRYEDFELGGTFKYSGWVESSDNDEHYDPKGRITYRSKVKDQNYYSVAVNAGYYVTPNAKVYVEGAWNRVTNKKGNTSLYDHNNNTSDYSKNGAGIENYNFITTAGLKYTF 297
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Membrane and cell surface proteins and peptides (2046)

Fold: Transmembrane beta-barrels (143)

Superfamily: OMPT-like (6)

Family: Outer membrane protease OMPT (1)

Protein domain: Outer membrane protease OMPT (1)

Escherichia coli [TaxId: 562] (1)

1a	d1i78a_	A:
1b	d1i78b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: OMPT-like (4)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (1)

1a	1i78B00	B:11-297
1b	1i78A00	A:1-297

(no "Pfam Domain" information available for 1I78)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OMPT_ECOLI | P09169)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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: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).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	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:0031230	intrinsic component of cell outer membrane	The component of the cell outer 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.

Asymmetric Unit
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	Cis Peptide Bonds
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	1i78
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	3.4.21.87
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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