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(-) Description

Title :  PENICILLIN ACYLASE WITH PHENYL PROPRIONIC ACID
 
Authors :  C. M. H. Hensgens, E. Keizer, H. J. Snijder, B. W. Dijkstra
Date :  19 Oct 01  (Deposition) - 02 Sep 03  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ntn-Hydrolase Fold, Helices, Beta-Strands, Phenyl Proprionic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. B. L. Alkema, C. M. H. Hensgens, H. J. Snijder, E. Keizer, B. W. Dijkstra, D. B. Janssen
Structural And Kinetic Studies On Ligand Binding In Wild-Type And Active-Site Mutants Of Penicillin Acylase.
Protein Eng. Des. Sel. V. 17 473 2004
PubMed-ID: 15254299  |  Reference-DOI: 10.1093/PROTEIN/GZH057

(-) Compounds

Molecule 1 - PENICILLIN ACYLASE ALPHA SUBUNIT
    Chains: A
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PENICILLIN G AMIDASE, PENICILLIN G AMIDOHYDROLASE
 
Molecule 2 - PENICILLIN ACYLASE BETA SUBUNIT
    Chains: B
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PENICILLIN G AMIDASE, PENICILLIN G AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GRO1Ligand/IonR-2-PHENYL-PROPRIONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:152 , ASP B:73 , VAL B:75 , ASP B:76 , PRO B:205 , ASP B:252BINDING SITE FOR RESIDUE CA B 702
2AC2SOFTWAREMET A:142 , PHE A:146 , SER B:1 , GLN B:23 , PHE B:24 , ALA B:69 , PHE B:71 , ASN B:241 , HOH B:1036BINDING SITE FOR RESIDUE GRO B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K7D)

(-) 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 1K7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K7D)

(-) Exons   (0, 0)

(no "Exon" information available for 1K7D)

(-) 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: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 d1k7d.1 A:,B: Penicillin acylase                                                                                                                                                                               SCOP domains
               CATH domains 1k7dA01 A:3-149 Penicillin Amidohydrolase, domain 1                                                                                                1k7dA02 A:150-179             ----------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7d 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 d1k7d.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1k7dB01 B:1-72,B:146-290,B:452-536                                      1k7dB02 B:73-145  [code=2.30.120.10, no name defined]                    1k7dB01 B:1-72,B:146-290,B:452-536 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                    1k7dB03 B:291-451  [code=1.10.1400.10, no name defined]                                                                                                          1k7dB01 B:1-72,B:146-290,B:452-536                                                   --------------------- CATH domains
           Pfam domains (1) Penicil_amidase-1k7dB01 B:1-549                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -------- Pfam domains (1)
           Pfam domains (2) Penicil_amidase-1k7dB02 B:1-549                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -------- Pfam domains (2)
         Sec.struct. author .eeeee.........eeeeee..........eeeeeeee..eeeeeeee.......eee...eeeeeee.....eeeeeee.......eeee..eeee.eeeeeee.......eeeeeeee..ee.........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...eee..hhhhhhh.eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k7d B   1 SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAYTYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYLHNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASLLAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPGTGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINLLNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISVGAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMALTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFIAPDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR 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 '|'

 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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NTN (93)

(-) 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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  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 1gm7 1gm8 1gm9 1h2g 1jx9 1k5q 1k5s 1kec 1pnk 1pnl 1pnm

(-) Related Entries Specified in the PDB File

1jx9 PA MUTANT
1k5q PA MUTANT WITH PHENYL ACETIC ACID.
1k5s PA MUTANT WITH PHENYL PROPRIONIC ACID.
1pnk PA