1E3A - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   A SLOW PROCESSING PRECURSOR PENICILLIN ACYLASE FROM ESCHERICHIA COLI

Authors :   L. Hewitt, V. Kasche, K. Lummer, R. J. Lewis, G. N. Murshudov, C. S. Verma, G. G. Dodson, K. S. Wilson

Date :   07 Jun 00 (Deposition) - 29 Nov 00 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Antibiotic Resistance, Amidase, Ntn-Hydrolase, Hydrolysis Of Penicillin G Acylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Hewitt, V. Kasche, K. Lummer, R. J. Lewis, G. N. Murshudov, C. S. Verma, G. G. Dodson, K. S. Wilson
Structure Of A Slow Processing Precursor Penicillin Acylase From Escherichia Coli Reveals The Linker Peptide Blocking The Active-Site Cleft
J. Mol. Biol. V. 302 887 2000
PubMed-ID: 10993730 | Reference-DOI: 10.1006/JMBI.2000.4105
(for further references see the PDB file header)

Molecule 1 - PENICILLIN AMIDASE ALPHA SUBUNIT
	Atcc	:	11105
	Cellular Location	:	PERIPLASM
	Chains	:	A
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Atcc Number	:	11105
	Expression System Gene	:	PAC
	Expression System Plasmid	:	PHM12
	Expression System Strain	:	K5
	Expression System Taxid	:	562
	Fragment	:	PENICILLIN AMIDASE RESIDUES 29-286
	Gene	:	PAC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Plasmid	:	PHM12
	Strain	:	HB101
	Synonym	:	PGA

Molecule 2 - PENICILLIN AMIDASE BETA SUBUNIT
	Atcc	:	11105
	Cellular Location	:	PERIPLASM
	Chains	:	B
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Atcc Number	:	11105
	Expression System Gene	:	PAC
	Expression System Plasmid	:	PHM12
	Expression System Strain	:	K5
	Expression System Taxid	:	562
	Fragment	:	PENICILLIN AMIDASE RESIDUES 287-846
	Gene	:	PAC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Plasmid	:	PHM12
	Strain	:	HB101
	Synonym	:	PGA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:187 , THR A:188 , ALA B:501 , ASP B:531 , HOH B:2854	BINDING SITE FOR RESIDUE EDO B 903
2	AC2	SOFTWARE	SER B:264 , SER B:330 , THR B:331 , ALA B:332	BINDING SITE FOR RESIDUE EDO B 904
3	AC3	SOFTWARE	PHE B:519 , LEU B:520 , ASN B:651 , LYS B:657 , HOH B:2470 , HOH B:2856	BINDING SITE FOR RESIDUE EDO B 905
4	AC4	SOFTWARE	GLU A:152 , ASP B:336 , VAL B:338 , ASP B:339 , PRO B:468 , ASP B:515	BINDING SITE FOR RESIDUE CA B 901
5	AC5	SOFTWARE	ALA A:254 , HOH A:2327 , VAL B:654 , HOH B:2464	BINDING SITE FOR RESIDUE CL B 902

(no "SS Bond" information available for 1E3A)

Asymmetric/Biological Unit

No.	Residues
1	Ala B:291	-	Pro B:292
2	Met B:628	-	Pro B:629
3	Ala B:767	-	Pro B:768

(no "SAP(SNP)/Variant" information available for 1E3A)

(no "PROSITE Motif" information available for 1E3A)

(no "Exon" information available for 1E3A)

Asymmetric/Biological 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:258
 aligned with PAC_ECOLX | P06875 from UniProtKB/Swiss-Prot  Length:846

    Alignment length:258
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278        
            PAC_ECOLX    29 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTAALLPRYDLPAPMLDRPAKGADGALLALTAGKNRETIAAQFAQGGANGLAGY 286
               SCOP domains d1e3a.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1e3aA01 A:3-149 Penicillin Amidohydrolase, domain 1                                                                                                --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhh.hhhhh......hhhhhh............hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e3a A   3 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTAALLPRYDLPAPMLDRPAKGADGALLALAAGKNRETIAAQFAQGGANGLAGY 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

Chain B from PDB  Type:PROTEIN  Length:560
 aligned with PAC_ECOLX | P06875 from UniProtKB/Swiss-Prot  Length:846

    Alignment length:560
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846
            PAC_ECOLX   287 PTTSNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 846
               SCOP domains d1e3a.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---1e3aB01 B:264-335,B:409-553,B:715-799                                   1e3aB02 B:336-408  [code=2.30.120.10, no name defined]                   1e3aB01 B:264-335,B:409-553,B:715-799 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                 1e3aB03 B:554-714  [code=1.10.1400.10, no name defined]                                                                                                          1e3aB01 B:264-335,B:409-553,B:715-799                                                --------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhh.....eeeeeeee........eeeeeeee..eeeeeeee.......eee...eeeeeee.....eeeeeee.......eeee..eeee.eeeeeee.......eeeeeee....eeeeee....eeeeeee....hhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee....eeeeee............................hhhhh.eee.....eeee.......................hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh..hhhhhh..................hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhh......eee...........hhhhheee.........eeeeee........eeeeee.....................hhhhhhh........hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3a B 261 PTGSNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 820
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ntn hydrolase-like (356)

Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) (352)

Family: Penicillin acylase, catalytic domain (37)

Protein domain: Penicillin acylase (25)

Escherichia coli [TaxId: 562] (24)

d1e3a.1

A:,B:

(no "Pfam Domain" information available for 1E3A)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PAC_ECOLX | P06875)

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:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008953	penicillin amidase activity	Catalysis of the reaction: penicillin + H2O = a carboxylate + 6-aminopenicillanate.
biological process
	GO:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0046677	response to antibiotic	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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala B:291 - Pro B:292	[ RasMol ]
		Ala B:767 - Pro B:768	[ RasMol ]
		Met B:628 - Pro B:629	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1e3a
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PAC_ECOLX \| P06875
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.1.11
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PAC_ECOLX \| P06875
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (4, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File