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(-) Description

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 :  1.45
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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric/Biological Unit (4, 23)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO20Ligand/Ion1,2-ETHANEDIOL
3PNN1Ligand/IonPENICILLIN G
4SME1Mod. Amino AcidMETHIONINE SULFOXIDE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:142 , PHE A:146 , SER A:149 , SER B:1 , GLN B:23 , PHE B:24 , ALA B:69 , PHE B:71 , EDO B:1562 , EDO B:1575 , HOH B:2450 , HOH B:2672 , HOH B:2673 , HOH B:2674 , HOH B:2675 , HOH B:2677BINDING SITE FOR RESIDUE PNN B1577
02AC2SOFTWAREGLU A:152 , ASP B:73 , VAL B:75 , ASP B:76 , PRO B:205 , ASP B:252BINDING SITE FOR RESIDUE CA B1576
03AC3SOFTWAREVAL A:182 , LYS A:200 , PHE A:201 , GLN A:203 , HOH A:2088 , HOH A:2251BINDING SITE FOR RESIDUE EDO A1210
04AC4SOFTWARETHR A:150 , SER A:151 , GLU A:152 , ILE A:153 , HOH A:2252 , HOH B:2184BINDING SITE FOR RESIDUE EDO A1211
05AC5SOFTWAREPRO A:187 , THR A:188 , ALA B:238 , VAL B:264 , ASP B:268 , HOH B:2649BINDING SITE FOR RESIDUE EDO B1558
06AC6SOFTWAREALA B:241 , PHE B:256 , LEU B:257 , ASN B:388 , LYS B:394 , HOH B:2318 , HOH B:2454BINDING SITE FOR RESIDUE EDO B1559
07AC7SOFTWAREPHE A:146 , SER A:147 , ASP A:148 , SER A:149 , HOH A:2167 , ALA B:69 , GLY B:70 , PHE B:71 , THR B:176 , HOH B:2650 , HOH B:2651BINDING SITE FOR RESIDUE EDO B1560
08AC8SOFTWAREALA B:79 , PRO B:208 , PRO B:210BINDING SITE FOR RESIDUE EDO B1561
09AC9SOFTWAREALA B:255 , PNN B:1577 , HOH B:2653 , HOH B:2654BINDING SITE FOR RESIDUE EDO B1562
10BC1SOFTWARETYR A:197 , PHE A:201 , ASP B:73 , ARG B:199 , LEU B:221 , HOH B:2261 , HOH B:2312BINDING SITE FOR RESIDUE EDO B1563
11BC2SOFTWAREASP B:327 , ILE B:329 , EDO B:1566 , HOH B:2656BINDING SITE FOR RESIDUE EDO B1564
12BC3SOFTWAREGLN A:37 , ASP A:38 , SER B:508 , ASP B:518 , HOH B:2657BINDING SITE FOR RESIDUE EDO B1565
13BC4SOFTWAREGLN B:288 , ARG B:291 , ILE B:329 , EDO B:1564 , HOH B:2658BINDING SITE FOR RESIDUE EDO B1566
14BC5SOFTWARELYS A:179 , HOH A:2203 , ASP B:73 , PRO B:205 , ARG B:206 , ALA B:250 , SER B:251 , ASP B:252BINDING SITE FOR RESIDUE EDO B1567
15BC6SOFTWARELYS B:10 , GLU B:272 , HOH B:2659BINDING SITE FOR RESIDUE EDO B1568
16BC7SOFTWARETHR A:125 , GLN B:273 , LYS B:274 , HOH B:2661 , HOH B:2662 , HOH B:2663BINDING SITE FOR RESIDUE EDO B1569
17BC8SOFTWAREGLY B:375 , SER B:386 , LEU B:387 , ASN B:388 , SER B:390 , HOH B:2664 , HOH B:2665BINDING SITE FOR RESIDUE EDO B1570
18BC9SOFTWARESER B:290 , ARG B:291 , ASN B:330 , TRP B:339 , LEU B:387 , ASN B:478 , HOH B:2356 , HOH B:2666BINDING SITE FOR RESIDUE EDO B1571
19CC1SOFTWAREARG B:291 , GLU B:475 , GLU B:529 , ASN B:530 , HOH B:2604 , HOH B:2667BINDING SITE FOR RESIDUE EDO B1572
20CC2SOFTWARETYR A:197 , HOH A:2229 , GLU B:224 , MET B:225 , ASN B:226 , PRO B:227 , LYS B:228 , GLN B:245 , HOH B:2668BINDING SITE FOR RESIDUE EDO B1573
21CC3SOFTWARELEU B:270 , GLN B:273 , LYS B:274 , GLN B:281 , HOH B:2669 , HOH B:2670BINDING SITE FOR RESIDUE EDO B1574
22CC4SOFTWAREPHE B:71 , ARG B:263 , SER B:386 , ASN B:388 , PNN B:1577 , HOH B:2665 , HOH B:2671 , HOH B:2672BINDING SITE FOR RESIDUE EDO B1575

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GM7)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GM7)

(-) Exons   (0, 0)

(no "Exon" information available for 1GM7)

(-) Sequences/Alignments

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 d1gm7.1 A:,B: Penicillin acylase                                                                                                                                                                                SCOP domains
               CATH domains 1gm7A01 A:3-149 Penicillin Amidohydrolase, domain 1                                                                                                1gm7A02 A:150-179             ------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........................hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gm7 A   3 SSSEIKIVRDEYGmPHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGKDFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFNTFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKWLVNPSAPTTIAVQESNYPLKFNQQNSQTA 209
                                    12   |    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
                                        16-SME                                                                                                                                                                                             


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 d1gm7.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gm7B01 B:1-72,B:146-290,B:452-536                                      1gm7B02 B:73-145  [code=2.30.120.10, no name defined]                    1gm7B01 B:1-72,B:146-290,B:452-536 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                    1gm7B03 B:291-451  [code=1.10.1400.10, no name defined]                                                                                                          1gm7B01 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.......................hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhh............ee..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.................hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.hhhhh.ee...eee...........hhhhheee.........eeeeee........eeeeee.....................hhhhhhh...ee...hhhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gm7 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)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GM7)

(-) Gene Ontology  (7, 7)

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).

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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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  1gm7
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  PAC_ECOLX | P06875
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  3.5.1.11
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAC_ECOLX | P06875: 1ai4 1ai5 1ai6 1ai7 1ajn 1ajp 1ajq 1e3a 1fxh 1fxv 1gk9 1gkf 1gm8 1gm9 1h2g 1jx9 1k5q 1k5s 1k7d 1kec 1pnk 1pnl 1pnm

(-) Related Entries Specified in the PDB File

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
1gm8 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