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Asym./Biol. Unit (Jmol Viewer)

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Title :   PENICILLIN ACYLASE COMPLEXED WITH M-NITROPHENYLACETIC ACID

Authors :   S. H. Done

Date :   01 May 97 (Deposition) - 12 Nov 97 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

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

Reference :   S. H. Done, J. A. Brannigan, P. C. E. Moody, R. E. Hubbard
Ligand-Induced Conformational Change In Penicillin Acylase.
J. Mol. Biol. V. 284 463 1998
PubMed-ID: 9813130 | Reference-DOI: 10.1006/JMBI.1998.2180
(for further references see the PDB file header)

Molecule 1 - PENICILLIN AMIDOHYDROLASE
	Atcc	:	11105
	Chains	:	A
	EC Number	:	3.5.1.11
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - PENICILLIN AMIDOHYDROLASE
	Atcc	:	11105
	Chains	:	B
	EC Number	:	3.5.1.11
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		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	MNP	1	Ligand/Ion	2-(3-NITROPHENYL)ACETIC ACID

Asymmetric Unit (4, 4)

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 B 558
2	AC2	SOFTWARE	SER B:1 , PRO B:22 , PHE B:24 , SER B:67 , ALA B:69 , ASN B:241 , HOH B:1018	BINDING SITE FOR RESIDUE MNP B 559
3	CAA	UNKNOWN	ASP B:73 , VAL B:75 , ASP B:76 , GLU A:152 , PRO B:205 , ASP B:252	CALCIUM ION BINDING SITE.
4	CAT	UNKNOWN	SER B:1 , ALA B:69 , GLN B:23 , ASN B:241	ACTIVE SITE.

(no "SS Bond" information available for 1AI5)

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 1AI5)

(no "PROSITE Motif" information available for 1AI5)

(no "Exon" information available for 1AI5)

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:206
 aligned with PAC_ECOLX | P06875 from UniProtKB/Swiss-Prot  Length:846

    Alignment length:206
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
            PAC_ECOLX    29 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQT 234
               SCOP domains d1ai5.1 A:,B: Penicillin acylase                                                                                                                                                                               SCOP domains
               CATH domains 1ai5A01 A:3-149 Penicillin Amidohydrolase, domain 1                                                                                                1ai5A02 A:150-179             ----------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeee...hhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhh....hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhh.............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ai5 A   3 SSSEIKIVRDEYGMPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQT 208
                                    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 d1ai5.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1ai5B01 B:1-72,B:146-290,B:452-536                                      1ai5B02 B:73-145  [code=2.30.120.10, no name defined]                    1ai5B01 B:1-72,B:146-290,B:452-536 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                    1ai5B03 B:291-451  [code=1.10.1400.10, no name defined]                                                                                                          1ai5B01 B:1-72,B:146-290,B:452-536                                                   --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeeee..........eeeeeeee..eeeeeeee.......eee...eeeeeee.....eeeeeee.......eeee..eeee.eeeeeee.......eeeeeeee..eeeeeee....eeeeeee.....hhhhhhhhhh......hhhhhhhhhh..eeeeeeeee....eeeeeee.................................eee.....eeee.........................hhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhh............eeeee...............eeeee........eeeeeee......eeeee.......................hhhhhh.........hhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ai5 B   1 SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQQWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 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)

d1ai5.1

A:,B:

(no "Pfam Domain" information available for 1AI5)

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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	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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Description

Compounds

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Ligands, Modified Residues, Ions (2, 2)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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