3IIQ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC ANALYSIS OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR

Authors :   M. Paetzel

Date :   03 Aug 09 (Deposition) - 01 Sep 09 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Ser/Lys Dyad, Lipopeptide, Serine Protease, Biaryl Bridge, Morpholino Beta-Sultam, Antibiotic, Peptidase, Hydrolase-Antibiotic-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Luo, P. Roussel, J. Dreier, M. G. Page, M. Paetzel
Crystallographic Analysis Of Bacterial Signal Peptidase In Ternary Complex With Arylomycin A2 And A Beta-Sultam Inhibitor.
Biochemistry V. 48 8976 2009
PubMed-ID: 19655811 | Reference-DOI: 10.1021/BI9009538

Molecule 1 - SIGNAL PEPTIDASE I
	Chains	:	A, B
	EC Number	:	3.4.21.89
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 76-323, PERIPLASMIC DOMAIN
	Gene	:	LEPB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	SPASE I, LEADER PEPTIDASE I

Molecule 2 - ARYLOMYCIN A2
	Chains	:	C, D
	Organism Scientific	:	STREPTOMYCES SP.
	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 (8, 18)

No.	Name	Count	Type	Full Name
1	5PG	2	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	CCN	2	Ligand/Ion	ACETONITRILE
3	DAL	2	Mod. Amino Acid	D-ALANINE
4	DSE	2	Mod. Amino Acid	N-METHYL-D-SERINE
5	GOL	4	Ligand/Ion	GLYCEROL
6	JZA	2	Ligand/Ion	4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-YL)CARBONYL]MORPHOLINE
7	M12	2	Ligand/Ion	10-METHYLUNDECANOIC ACID
8	TRT	2	Ligand/Ion	FRAGMENT OF TRITON X-100

Biological Unit 1 (6, 6)

No.	Name	Count	Type	Full Name
1	5PG	1	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	CCN	-1	Ligand/Ion	ACETONITRILE
3	DAL	1	Mod. Amino Acid	D-ALANINE
4	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
5	GOL	-1	Ligand/Ion	GLYCEROL
6	JZA	1	Ligand/Ion	4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-YL)CARBONYL]MORPHOLINE
7	M12	1	Ligand/Ion	10-METHYLUNDECANOIC ACID
8	TRT	1	Ligand/Ion	FRAGMENT OF TRITON X-100

Biological Unit 2 (8, 12)

No.	Name	Count	Type	Full Name
1	5PG	1	Mod. Amino Acid	(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2	CCN	2	Ligand/Ion	ACETONITRILE
3	DAL	1	Mod. Amino Acid	D-ALANINE
4	DSE	1	Mod. Amino Acid	N-METHYL-D-SERINE
5	GOL	4	Ligand/Ion	GLYCEROL
6	JZA	1	Ligand/Ion	4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-YL)CARBONYL]MORPHOLINE
7	M12	1	Ligand/Ion	10-METHYLUNDECANOIC ACID
8	TRT	1	Ligand/Ion	FRAGMENT OF TRITON X-100

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:88 , SER A:90 , ASN A:277 , SER A:278 , ALA A:279 , GLU A:307 , TYR C:6	BINDING SITE FOR RESIDUE JZA A 324
02	AC2	SOFTWARE	GLU A:104 , THR A:297 , GOL A:326	BINDING SITE FOR RESIDUE TRT A 325
03	AC3	SOFTWARE	TRT A:325	BINDING SITE FOR RESIDUE GOL A 326
04	AC4	SOFTWARE	ARG A:236 , GOL A:328 , GOL A:329	BINDING SITE FOR RESIDUE GOL A 327
05	AC5	SOFTWARE	GLY A:321 , ILE A:322 , HIS A:323 , GOL A:327 , CCN A:330 , ASN B:186	BINDING SITE FOR RESIDUE GOL A 328
06	AC6	SOFTWARE	SER A:317 , ARG A:318 , GOL A:327 , HOH A:2127 , HOH A:2128	BINDING SITE FOR RESIDUE GOL A 329
07	AC7	SOFTWARE	THR A:94 , ILE A:322 , HIS A:323 , GOL A:328 , CCN A:331	BINDING SITE FOR RESIDUE CCN A 330
08	AC8	SOFTWARE	THR A:94 , HIS A:235 , ARG A:236 , HIS A:323 , CCN A:330 , HOH A:2079	BINDING SITE FOR RESIDUE CCN A 331
09	AC9	SOFTWARE	SER B:88 , SER B:90 , LYS B:145 , ASN B:277 , SER B:278 , ALA B:279 , GLU B:307 , TRT B:325 , TYR D:6	BINDING SITE FOR RESIDUE JZA B 324
10	BC1	SOFTWARE	PHE A:196 , PHE B:196 , ASP B:276 , ASN B:277 , SER B:278 , ALA B:279 , TYR B:283 , JZA B:324	BINDING SITE FOR RESIDUE TRT B 325
11	BC2	SOFTWARE	GLU A:82 , PRO A:83 , PHE A:84 , GLN A:85 , PRO A:87 , SER A:88 , SER A:90 , ASP A:142 , TYR A:143 , ILE A:144 , LYS A:145 , JZA A:324 , HOH A:2002 , HOH A:2024 , HOH A:2025 , HOH C:2002	BINDING SITE FOR CHAIN C OF ARYLOMYCIN A2
12	BC3	SOFTWARE	GLU B:82 , PRO B:83 , PHE B:84 , GLN B:85 , PRO B:87 , ASP B:142 , TYR B:143 , ILE B:144 , LYS B:145 , JZA B:324 , HOH B:2020 , HOH B:2022 , HOH D:2001 , HOH D:2003 , HOH D:2004	BINDING SITE FOR CHAIN D OF ARYLOMYCIN A2

Asymmetric Unit

No.	Residues
1	A:170	-	A:176
2	B:170	-	B:176

Asymmetric Unit

No.	Residues
1	Met A:92	-	Pro A:93
2	Met B:92	-	Pro B:93
3	Ser B:172	-	Gly B:173
4	Cys B:176	-	Glu B:177

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

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 3IIQ)

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:217
 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 d3iiqa_ A: Type 1 signal pep                 tidase                                                                                                                                                                                                   SCOP domains
               CATH domains 3iiqA01 A:79-153,A:263-319 U                 mud Fragment, subunit A       3iiqA02 A:154-188,   A:224-262     ---------        ------------------3iiqA02 A:154-188,A:224-262            3iiqA01 A:79-153,A:263-319 Umud Fragment, subunit A      ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.............eeeeeee.-----------------......eeeee.......eeeeeeee....eeeee....eeeee....---.......eee...eeeeeeee..--------.eeee.........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
                 3iiq A  79 FIYEPFQIPSGSMMPTLLIGDFILVEKF-----------------HPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCS---ACENALPVTYSNVEPSDFVQTFS--------SGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 323
                                    88        98       | -         -     | 128       138       148       158       168  |   |178       188        |-       208       218       228       238       248       258       268       278       288       298       308       318     
                                                     106               124                                            171 175                   197      206

Chain B from PDB  Type:PROTEIN  Length:224
 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 d3iiqb_ B: Type 1 signal pe               ptidase                                                                                                                                                                                                    SCOP domains
               CATH domains 3iiqB01 B:80-153,B:263-323                Umud Fragment, subunit A        3iiqB02 B:154-188,B:  224-262      ------------   --------------------3iiqB02 B:154-188,B:224-262            3iiqB01 B:80-153,B:263-323 Umud Fragment, subunit A           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.............eeeeeee.---------------........eeeee.......eeeeeeee....eeeee....eeeee......--......eee...eeeeeeeeee...---.eeeeee..........eeeeeeeeee..eeeeeee......hhhhh.........eee....eeeee........hhhhhh.ee...eeeeeeeeeeeeee.....eeee.hhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SPASE_I_-------------------------------------------------SPASE_I_2    --------------------------------------------------------------------------------------------------------------SPASE_I_3     ------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iiq B  80 IYEPFQIPSGSMMPTLLIGDFILVEKF---------------TGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSG--CENALPVTYSNVEPSDFVQTFSRRN---ATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH 323
                                    89        99      |  -         -  |    129       139       149       159       169   |  |179       189       199|   |  209       219       229       239       249       259       269       279       289       299       309       319    
                                                    106             122                                                173  |                     200 204                                                                                                                       
                                                                                                                          176

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
                 3iiq 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
                 3iiq 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(

)

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	d3iiqa_	A:
1b	d3iiqb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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: 83333. Strain: k-12. (1)

1a	3iiqB02	B:154-188,B:224-262
1b	3iiqA02	A:154-188,A:224-262

Architecture: Ribbon (789)

Topology: Umud Fragment, subunit A (13)

Homologous Superfamily: Umud Fragment, subunit A (13)

Escherichia coli. Organism_taxid: 83333. Strain: k-12. (1)

2a	3iiqA01	A:79-153,A:263-319
2b	3iiqB01	B:80-153,B:263-323

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

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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	Cis Peptide Bonds
		Cys B:176 - Glu B:177	[ RasMol ]
		Met A:92 - Pro A:93	[ RasMol ]
		Met B:92 - Pro B:93	[ RasMol ]
		Ser B:172 - Gly B:173	[ RasMol ]

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	3iiq
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	3.4.21.89
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	LEP_ECOLI \| P00803	:	1b12 1kn9 1t7d 3s04

1b12	CRYSTAL STRUCTUTE OF TYPE 1 SIGNAL PEPTIDASE COMPLEXED WITH BETA-LACTAM INHIBITOR
1kn9	CRYSTAL STRUCTURE OF SIGNAL PEPTIDASE APO_ENZYME
1t7d	CRYSTAL STRUCTUTE OF TYPE 1 SIGNAL PEPTIDASE COMPLEXED WITH ARYLOMYCIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 18)

Sites (12, 12)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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