3S04 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE IN COMPLEX WITH AN ARYLOMYCIN LIPOGLYCOPEPTIDE ANTIBIOTIC

Authors :   M. Paetzel, C. Luo

Date :   13 May 11 (Deposition) - 05 Oct 11 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.44

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

Keywords :   Mostly-Beta Fold, Membrane Bound, Serine Protease, Secreted Preproteins, Cytoplasmic Membrane, Hydrolase-Antibiotic Complex, Signal Peptidase, Leader Peptidase, Signal Peptide, Leader Peptide, Serine-Lysine Dyad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Liu, C. Luo, P. A. Smith, J. K. Chin, M. G. Page, M. Paetzel, F. E. Romesberg
Synthesis And Characterization Of The Arylomycin Lipoglycopeptide Antibiotics And The Crystallographic Analysis Of Their Complex With Signal Peptidase.
J. Am. Chem. Soc. V. 133 17869 2011
PubMed-ID: 21999324 | Reference-DOI: 10.1021/JA207318N

Molecule 1 - SIGNAL PEPTIDASE I
	Chains	:	A, B
	EC Number	:	3.4.21.89
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PERIPLASMIC DOMAIN, UNP RESIDUES 76-323
	Gene	:	B2568, JW2552, LEPB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	SPASE I, LEADER PEPTIDASE I

Molecule 2 - GLYCO-ARYLOMYCIN
	Chains	:	I, J
	Organism Scientific	:	STREPTOMYCES SP.
	Organism Taxid	:	1931

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	02U	2	Ligand/Ion	14-METHYLHEXADEC-9-ENOIC ACID
2	02V	2	Mod. Amino Acid	(2S)-(3,4-DIHYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
3	DAL	2	Mod. Amino Acid	D-ALANINE
4	DSE	2	Mod. Amino Acid	N-METHYL-D-SERINE
5	RAM	2	Ligand/Ion	ALPHA-L-RHAMNOSE

Biological Unit 1 (5, 5)

No.	Name	Count	Type	Full Name
1	02U	1	Ligand/Ion	14-METHYLHEXADEC-9-ENOIC ACID
2	02V	1	Mod. Amino Acid	(2S)-(3,4-DIHYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
3	DAL	1	Mod. Amino Acid	D-ALANINE
4	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
5	RAM	1	Ligand/Ion	ALPHA-L-RHAMNOSE

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	02U	1	Ligand/Ion	14-METHYLHEXADEC-9-ENOIC ACID
2	02V	1	Mod. Amino Acid	(2S)-(3,4-DIHYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
3	DAL	1	Mod. Amino Acid	D-ALANINE
4	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
5	RAM	1	Ligand/Ion	ALPHA-L-RHAMNOSE

Biological Unit 3 (5, 5)

No.	Name	Count	Type	Full Name
1	02U	1	Ligand/Ion	14-METHYLHEXADEC-9-ENOIC ACID
2	02V	1	Mod. Amino Acid	(2S)-(3,4-DIHYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
3	DAL	1	Mod. Amino Acid	D-ALANINE
4	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
5	RAM	1	Ligand/Ion	ALPHA-L-RHAMNOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:83 , PHE A:85 , GLN A:86 , PRO A:88 , SER A:89 , SER A:91 , ASP A:143 , TYR A:144 , ILE A:145 , LYS A:146	BINDING SITE FOR CHAIN J OF GLYCO-ARYLOMYCIN
2	AC2	SOFTWARE	GLU B:83 , PRO B:84 , PHE B:85 , GLN B:86 , PRO B:88 , SER B:89 , SER B:91 , ASP B:143 , TYR B:144 , ILE B:145 , LYS B:146	BINDING SITE FOR CHAIN I OF GLYCO-ARYLOMYCIN

Asymmetric Unit

No.	Residues
1	A:171	-	A:177

Asymmetric Unit

No.	Residues
1	Met A:93	-	Pro A:94
2	Met B:93	-	Pro B:94

(no "SAP(SNP)/Variant" information available for 3S04)

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:89-96 B:89-96
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	2	A:146-158 B:146-158
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	2	A:269-282 B:269-282

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	A:89-96 -
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	1	A:146-158 -
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	1	A:269-282 -

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	- B:89-96
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	1	- B:146-158
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	1	- B:269-282

Biological Unit 3 (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:89-96 B:89-96
2	SPASE_I_2	PS00760	Signal peptidases I lysine active site.	LEP_ECOLI	146-158	2	A:146-158 B:146-158
3	SPASE_I_3	PS00761	Signal peptidases I signature 3.	LEP_ECOLI	269-282	2	A:269-282 B:269-282

(no "Exon" information available for 3S04)

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:209
 aligned with LEP_ECOLI | P00803 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:245
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319     
            LEP_ECOLI    80 FIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 324
               SCOP domains d3s04a_ A: Type 1 signal pept                idase                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.............eeeeeee..----------------......eeeee.......eeeeeeee....eeeee....eeeee....---.......eeee..eeeeeeee.--------..eeee.........eeeeeeeeeee..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
                 3s04 A  80 FIYEPFQIPSGSMMPTLLIGDFILVEKFA----------------HPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCS---ACENALPVTYSNVEPSDFVQTF--------TSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFD---------LRLSRIGGIH 324
                                    89        99        |-         -     | 129       139       149       159       169  |   |179       189       | -      |209       219       229       239       249       259       269       279       289       299     |   -     | 319     
                                                      108              125                                            172 176                  197      206                                                                                                305       315

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

    Alignment length:245
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319     
            LEP_ECOLI    80 FIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 324
               SCOP domains d3s04b_ B: Type 1 signal pept              idase                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.............eeeeeee..--------------........eeeee.......eeeeeeee....eeeee....eeeee...--------...eeee..eeeeeeeeeee.....eeeeeee..........eeeeeeeeee..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
                 3s04 B  80 FIYEPFQIPSGSMMPTLLIGDFILVEKFA--------------TGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGC--------ALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 324
                                    89        99        |-         -   |   129       139       149       159       169 |       -|      189       199       209       219       229       239       249       259       269       279       289       299       309       319     
                                                      108            123                                             171      180

Chain I from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3s04 I   2 xxGxAY   7
                            || |  
                            2-DSE 
                             3-DAL
                               5-02V

Chain J from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3s04 J   2 xxGxAY   7
                            || |  
                            || |  
                            2-DSE 
                             3-DAL
                               5-02V

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(

)

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	d3s04a_	A:
1b	d3s04b_	B:

(no "CATH Domain" information available for 3S04)

(no "Pfam Domain" information available for 3S04)

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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Access by PDB/NDB ID
	3s04
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	3.4.21.89
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UniProtKB/Swiss-Prot
	LEP_ECOLI \| P00803	:	1b12 1kn9 1t7d 3iiq

1b12	CRYSTAL STRUCTURE OF TYPE 1 SIGNAL PEPTIDASE FROM ESCHERICHIA COLI IN COMPLEX WITH A BETA-LACTAM INHIBITOR
1kn9	CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO- ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER -LYS DYAD MECHANISM.
1t7d	CRYSTAL STRUCTURE OF ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE IN COMPLEX WITH A LIPOPEPTIDE INHIBITOR
3iiq	CRYSTALLOGRAPHIC ANALYSIS OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR

Description

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Ligands, Modified Residues, Ions (5, 10)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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