1GM8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM

Authors :   C. E. Mcvey, M. A. Walsh, G. G. Dodson, K. S. Wilson, J. A. Brannigan

Date :   11 Sep 01 (Deposition) - 28 Nov 01 (Release) - 07 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Mcvey, M. A. Walsh, G. G. Dodson, K. S. Wilson, J. A. Brannigan
Crystal Structures Of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into The Catalytic Mechanism
J. Mol. Biol. V. 313 139 2001
PubMed-ID: 11601852 | Reference-DOI: 10.1006/JMBI.2001.5043
(for further references see the PDB file header)

Molecule 1 - PENICILLIN G ACYLASE ALPHA SUBUNIT
	Atcc	:	11105
	Cellular Location	:	PERIPLASM
	Chains	:	A
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	PAC
	Expression System Plasmid	:	PACYC184PAC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 27-235
	Gene	:	PAC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NTN, PENICILLIN AMIDOHYDROLASE

Molecule 2 - PENICILLIN G ACYLASE BETA SUBUNIT
	Atcc	:	11105
	Cellular Location	:	PERIPLASM
	Chains	:	B
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	PAC
	Expression System Plasmid	:	PACYC184PAC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 290-846
	Gene	:	PAC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NTN, PENICILLIN AMIDOHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SOX	1	Ligand/Ion	N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLACETAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:152 , ASP B:73 , VAL B:75 , ASP B:76 , PRO B:205 , ASP B:252	BINDING SITE FOR RESIDUE CA B1558
2	AC2	SOFTWARE	MET A:142 , PHE A:146 , SER A:149 , SER B:1 , GLN B:23 , PHE B:24 , ALA B:69 , PHE B:71 , HOH B:2459 , HOH B:2460 , HOH B:2461 , HOH B:2462	BINDING SITE FOR RESIDUE SOX B1559

(no "SS Bond" information available for 1GM8)

Asymmetric/Biological Unit

No.	Residues
1	Ala B:28	-	Pro B:29
2	Met B:365	-	Pro B:366
3	Ala B:504	-	Pro B:505

(no "SAP(SNP)/Variant" information available for 1GM8)

(no "PROSITE Motif" information available for 1GM8)

(no "Exon" information available for 1GM8)

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:207
 aligned with PAC_ECOLX | P06875 from UniProtKB/Swiss-Prot  Length:846

    Alignment length:207
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       
            PAC_ECOLX    29 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTA 235
               SCOP domains d1gm8.1 A:,B: Penicillin acylase                                                                                                                                                                                SCOP domains
               CATH domains 1gm8A01 A:3-149 Penicillin Amidohydrolase, domain 1                                                                                                1gm8A02 A:150-179             ------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee..............hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gm8 A   3 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTA 209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain B from PDB  Type:PROTEIN  Length:557
 aligned with PAC_ECOLX | P06875 from UniProtKB/Swiss-Prot  Length:846

    Alignment length:557
                                   299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       
            PAC_ECOLX   290 SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 846
               SCOP domains d1gm8.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gm8B01 B:1-72,B:146-290,B:452-536                                      1gm8B02 B:73-145  [code=2.30.120.10, no name defined]                    1gm8B01 B:1-72,B:146-290,B:452-536 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                    1gm8B03 B:291-451  [code=1.10.1400.10, no name defined]                                                                                                          1gm8B01 B:1-72,B:146-290,B:452-536                                                   --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.........eeeeee..........eeeeeeee..eeeeeeee.......eee...eeeeeee.....eeeeeee.......eeee..eeee.eeeeeee.......eeeeeeee..eeeeeee....eeeeeee....hhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee....eeeeee...ee..........ee........ee.hhhhh.eee.....eeee...eee..................hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh............ee..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.................hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhh.ee...eee...........hhhhheee.........eeeeee........eeeeee.....................hhhhhhh...ee...hhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gm8 B   1 SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWANSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 557
                                    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       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

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)

d1gm8.1

A:,B:

(no "Pfam Domain" information available for 1GM8)

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
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	Ligands, Modified Residues, Ions
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala B:28 - Pro B:29	[ RasMol ]
		Ala B:504 - Pro B:505	[ RasMol ]
		Met B:365 - Pro B:366	[ RasMol ]

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	1gm8
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	PAC_ECOLX \| P06875
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	3.5.1.11
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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1ai4	PENICILLIN ACYLASE COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETIC ACID
1ai5	PENICILLIN ACYLASE COMPLEXED WITH M-NITROPHENYLACETIC ACID
1ai6	PENICILLIN ACYLASE WITH P-HYDROXYPHENYLACETIC ACID
1ai7	PENICILLIN ACYLASE COMPLEXED WITH PHENOL
1ajn	PENICILLIN ACYLASE COMPLEXED WITH P-NITROPHENYLACETIC ACID
1ajp	PENICILLIN ACYLASE COMPLEXED WITH 2,5-DIHYDROXYPHENYLACETIC ACID
1ajq	PENICILLIN ACYLASE COMPLEXED WITH THIOPHENEACETIC ACID
1cp9	CRYSTAL STRUCTURE OF PENICILLIN G ACYLASE FROM THE BRO1 MUTANT STRAIN OF PROVIDENCIA RETTGERI
1e3a	A SLOW PROCESSING PRECURSOR PENICILLIN ACYLASE FROM ESCHERICHIA COLI
1fxh	MUTANT OF PENICILLIN ACYLASE IMPAIRED IN CATALYSIS WITH PHENYLACETIC ACID IN THE ACTIVE SITE
1fxv	PENICILLIN ACYLASE MUTANT IMPAIRED IN CATALYSIS WITHPENICILLIN G IN THE ACTIVE SITE
1gk9	CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
1gkf	CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
1gm7	CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
1gm9	CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
1pnk	PENICILLIN AMIDOHYDROLASE
1pnl	PENICILLIN AMIDOHYDROLASE
1pnm	PENICILLIN AMIDOHYDROLASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

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 (5, 5)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File