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Title :   GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE: MUTATIONAL STUDY OF ACTIVATION MECHANISM

Authors :   J. K. Kim, I. S. Yang, H. J. Shin, K. J. Cho, E. K. Ryu, S. H. Kim, S. S. Park, K

Date :   21 Jul 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Autoproteolysis, Precursor Activation, Intermediate Structure, Cephalosporin Acylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Kim, I. S. Yang, H. J. Shin, K. J. Cho, E. K. Ryu, S. H. Kim, S. S. Park, K. H. Kim
Insight Into Autoproteolytic Activation From The Structure Of Cephalosporin Acylase: A Protein With Two Proteolytic Chemistries.
Proc. Natl. Acad. Sci. Usa V. 103 1732 2006
PubMed-ID: 16446446 | Reference-DOI: 10.1073/PNAS.0507862103

Molecule 1 - GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE
	Chains	:	A
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ALPHA DOMAIN(RESIDUES 1-166)
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	405038
	Strain	:	GK16

Molecule 2 - GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE
	Chains	:	B
	EC Number	:	3.5.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BETA DOMAIN(RESIDUES 1-522)
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	405038
	Strain	:	GK16

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:148 , SER A:152 , PRO A:162 , HOH A:324 , PHE B:31	BINDING SITE FOR RESIDUE GOL A 301

(no "SS Bond" information available for 2AE3)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:130	-	Pro A:131
2	Trp B:252	-	Pro B:253
3	Thr B:378	-	Pro B:379
4	Thr B:465	-	Pro B:466

(no "SAP(SNP)/Variant" information available for 2AE3)

(no "PROSITE Motif" information available for 2AE3)

(no "Exon" information available for 2AE3)

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:159
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:159
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185         
           G7AC_PSEU7    36 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDL 194
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ae3A00 A:7-165 Penicillin Amidohydrolase, domain 1                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ae3 A   7 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDL 165
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain B from PDB  Type:PROTEIN  Length:522
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:522
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718  
           G7AC_PSEU7   199 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 720
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ae3B01 B:1-75,B:142-267,B:451-508                                         2ae3B02 B:76-141  [code=2.30.120.10, no name defined]             2ae3B01 B:1-75,B:142-267,B:451-508 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                 --2ae3B03 B:270-450  [code=1.10.1400.10, no name defined]                                                                                                                              2ae3B01 B:1-75,B:142-267,B:451-508                        -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhh.....eeeee.eee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee.....eeeeeee.....eeeeeee........eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eeee..............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ae3 B   1 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIKFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 522
                                    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

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 '\|'

(no "SCOP Domain" information available for 2AE3)

(no "Pfam Domain" information available for 2AE3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (G7AC_PSEU7 | P07662)

molecular function
	GO:0033968	glutaryl-7-aminocephalosporanic-acid acylase activity	Catalysis of the reaction: (7R)-7-(4-carboxybutanamido)cephalosporanate + H2O = (7R)-7-aminocephalosporanate + glutarate.
	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.
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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:130 - Pro A:131	[ RasMol ]
		Thr B:378 - Pro B:379	[ RasMol ]
		Thr B:465 - Pro B:466	[ RasMol ]
		Trp B:252 - Pro B:253	[ RasMol ]

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Access by PDB/NDB ID
	2ae3
		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
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Access by UniProt ID/Accession number
	G7AC_PSEU7 \| P07662
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.5.1.11
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	G7AC_PSEU7 \| P07662
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UniProtKB/Swiss-Prot
	G7AC_PSEU7 \| P07662	:	1gk0 1gk1 1or0 2adv 2ae4 2ae5 3s8r

2adv	THE SAME PROTEIN, ALPHA, BETA1 AND BETA2(Y33L) DOMAINS
2ae4	THE SAME PROTEIN, ALPHA(E159Q) AND BETA DOMAINS
2ae5	THE SAME PROTEIN, ALPHA AND BETA(S1C) DOMAINS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (4, 4)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Related Entries

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