1T7D - JenaLib

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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE IN COMPLEX WITH A LIPOPEPTIDE INHIBITOR

Authors :   M. Paetzel, J. J. Goodall, M. Kania, R. E. Dalbey, M. G. P. Page

Date :   09 May 04 (Deposition) - 13 Jul 04 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.47

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

Keywords :   Signal Peptidase, Ser/Lys Dyad, Hydrolase, Lipopeptide, Antibiotic, Biaryl Bridge, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Paetzel, J. J. Goodall, M. Kania, R. E. Dalbey, M. G. P. Page
Crystallographic And Biophysical Analysis Of A Bacterial Signal Peptidase In Complex With A Lipopeptide Based Inhibitor.
J. Biol. Chem. V. 279 30781 2004
PubMed-ID: 15136583 | Reference-DOI: 10.1074/JBC.M401686200
(for further references see the PDB file header)

Molecule 1 - SIGNAL PEPTIDASE I
	Chains	:	A, B
	EC Number	:	3.4.21.89
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 76-324
	Gene	:	LEPB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SPASE I, LEADER PEPTIDASE I

Molecule 2 - ARYLOMYCIN A2
	Chains	:	C, D
	Organism Scientific	:	STREPTOMYCES TU
	Organism Taxid	:	1931

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	5PG	2	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	DAL	2	Mod. Amino Acid	D-ALANINE
3	DSE	2	Mod. Amino Acid	N-METHYL-D-SERINE
4	M12	2	Ligand/Ion	10-METHYLUNDECANOIC ACID

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	5PG	1	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	DAL	1	Mod. Amino Acid	D-ALANINE
3	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
4	M12	1	Ligand/Ion	10-METHYLUNDECANOIC ACID

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	5PG	1	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	DAL	1	Mod. Amino Acid	D-ALANINE
3	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
4	M12	1	Ligand/Ion	10-METHYLUNDECANOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:82 , PRO A:83 , GLN A:85 , PRO A:87 , SER A:90 , ASP A:142 , TYR A:143 , ILE A:144 , LYS A:145 , HOH A:2005 , HOH A:2006	BINDING SITE FOR CHAIN C OF ARYLOMYCIN A2
2	AC2	SOFTWARE	PRO B:83 , PHE B:84 , GLN B:85 , PRO B:87 , SER B:88 , SER B:90 , ASP B:142 , TYR B:143 , ILE B:144 , LYS B:145 , HOH D:2002 , HOH D:2003	BINDING SITE FOR CHAIN D OF ARYLOMYCIN A2

Asymmetric Unit

No.	Residues
1	B:170	-	B:176

Asymmetric Unit

No.	Residues
1	Met A:92	-	Pro A:93
2	Met B:92	-	Pro B:93

(no "SAP(SNP)/Variant" information available for 1T7D)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SPASE_I_1	PS00501	Signal peptidases I serine active site.	LEP_ECOLI	89-96	2	A:88-95 B:88-95
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	2	A:145-157 B:145-157
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	2	A:268-281 B:268-281

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SPASE_I_1	PS00501	Signal peptidases I serine active site.	LEP_ECOLI	89-96	1	- B:88-95
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	1	- B:145-157
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	1	- B:268-281

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SPASE_I_1	PS00501	Signal peptidases I serine active site.	LEP_ECOLI	89-96	1	A:88-95 -
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	1	A:145-157 -
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	1	A:268-281 -

(no "Exon" information available for 1T7D)

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:208
 aligned with LEP_ECOLI | P00803 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:244
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
            LEP_ECOLI    81 IYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 324
               SCOP domains d1t7da_ A: Type 1 signal pe                 ptidase                                                                                                                                                                                                  SCOP domains
               CATH domains 1t7dA01 A:80-153,A:263-323                  Umud Fragment, subunit A      1t7dA02 A:154-262         [code=2.170.230.10,    no name defined]                                            1t7dA01 A:80-153,A:263-323 Umud Fragment,          subunit A  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.............eeeeeee.-----------------......eeeee.......eeeeeeee....eeeee....eeeee...-------....eee...eeeeeeeeeee.---.eeeeeee..........eeeeeeeeee..eeeeeee......hhhhh.........eee....eeeee........hhhhhh.ee...eeeeeeeeeee..---------.hhhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SPASE_I_-------------------------------------------------SPASE_I_2    --------------------------------------------------------------------------------------------------------------SPASE_I_3     ------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t7d A  80 IYEPFQIPSGSMMPTLLIGDFILVEKF-----------------HPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGC-------NALPVTYSNVEPSDFVQTFSRR---EATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFD---------LRLSRIGGIH 323
                                    89        99      |  -         -    |  129       139       149       159       169|      179       189       199   |   209       219       229       239       249       259       269       279       289       299    |    -    |  319    
                                                    106               124                                           170     178                  199 203                                                                                                  304       314

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with LEP_ECOLI | P00803 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:244
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
            LEP_ECOLI    81 IYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 324
               SCOP domains d1t7db_ B: Type 1 signal pep             tidase                                                                                                                                                                                                      SCOP domains
               CATH domains 1t7dB01 B:80-153,B:263-321 U             mud Fragment, subunit A          1t7dB02 B:154-188,B:224-262        ---------        ------------------1t7dB02 B:154-188,B:224-262            1t7dB01 B:80-153,B:263-321 Umud Fragment, subunit A        -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.............eeeeeee..-------------.........eeeee.......eeeeeeee....eeeee....eeeee..............eee...eeeeeeee..--------..eee.........eeeeeeeeeee..eeeeeee......hhhhh.........eee....eeeee........hhhhhh.ee...eeeeeeeeeeeee........ee.hhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SPASE_I_-------------------------------------------------SPASE_I_2    --------------------------------------------------------------------------------------------------------------SPASE_I_3     ------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t7d B  80 IYEPFQIPSGSMMPTLLIGDFILVEKFA-------------ETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFS--------SGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 323
                                    89        99       | -         - |     129       139       149       159       169       179       189       | -      |209       219       229       239       249       259       269       279       289       299       309       319    
                                                     107           121                                                                         197      206

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 1t7d C   1 xxGxAY   6
                            || |  
                            1-DSE 
                             2-DAL
                               4-5PG

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               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
                 1t7d D   1 xxGxAY   6
                            || |  
                            || |  
                            1-DSE 
                             2-DAL
                               4-5PG

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(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: LexA/Signal peptidase (17)

Superfamily: LexA/Signal peptidase (17)

Family: Type 1 signal peptidase (5)

Protein domain: Type 1 signal peptidase (5)

Escherichia coli [TaxId: 562] (5)

1a	d1t7da_	A:
1b	d1t7db_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Signal Peptidase I; Chain: A, domain 2 (4)

Homologous Superfamily: [code=2.170.230.10, no name defined] (4)

Escherichia coli. Organism_taxid: 562. (1)

1a	1t7dB02	B:154-188,B:224-262
1b	1t7dA02	A:154-262

Architecture: Ribbon (789)

Topology: Umud Fragment, subunit A (13)

Homologous Superfamily: Umud Fragment, subunit A (13)

Escherichia coli. Organism_taxid: 562. (6)

2a	1t7dA01	A:80-153,A:263-323
2b	1t7dB01	B:80-153,B:263-321

(no "Pfam Domain" information available for 1T7D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LEP_ECOLI | P00803)

molecular function
	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).
	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).
	GO:0015643	toxic substance binding	Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006465	signal peptide processing	The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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 Unit
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		Met B:92 - Pro B:93	[ RasMol ]

Biological Units
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	1t7d
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	LEP_ECOLI \| P00803	:	1b12 1kn9 3iiq 3s04

1b12	CRYSTAL STRUCTUTE OF TYPE 1 SIGNAL PEPTIDASE COMPLEXED WITH BETA-LACTAM INHIBITOR
1kn9	CRYSTAL STRUCTURE OF SIGNAL PEPTIDASE APO_ENZYME
3iiq	CRYSTAL STRUCURE OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR

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