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(-) Description

Title :  STRUCTURE OF TRUNCATED MUTANT CYS1GLY OF PENICILLIN V ACYLASE FROM BACILLUS SPHAERICUS CO-CRYSTALLIZED WITH PENICILLIN V
 
Authors :  M. C. Pathak, J. Brannigan, G. G. Dodson, C. G. Suresh
Date :  10 Aug 07  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Zymogen, Hydrolase, Precursor, Penicillin, Autoproteolysis, Antibiotic Resistance, Catalysis, Penicillin V Acylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Pathak, J. Brannigan, G. G. Dodson, C. G. Suresh
Studies On The Catalysis And Post Translational Processing Of Penicillin V Acylase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN ACYLASE
    Chains: A, C
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS SPHAERICUS
    Strain: NCIM 2478
    Synonym: PENICILLIN V AMIDASE, PVA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PNV2Ligand/Ion(2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PNV4Ligand/Ion(2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , TYR A:82 , ASN A:175 , PRO A:225 , ARG A:228 , GLU A:270 , ASP A:274 , GLY C:211 , GLN C:212BINDING SITE FOR RESIDUE PNV A 903
2AC2SOFTWAREGLY A:211 , GLN A:212 , ASP C:20 , TYR C:82 , ASN C:175 , ARG C:228 , THR C:268 , ASN C:269 , GLU C:270 , LYS C:272 , ASP C:274BINDING SITE FOR RESIDUE PNV C 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z71)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:176 -Pro A:177
2Ser C:176 -Pro C:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z71)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z71)

(-) Sequences/Alignments

Asymmetric 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:330
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:330
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQ 333
               SCOP domains d2z71a_ A: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2z71A00 A:1-330 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....eeeeeeeee......eeeee....eee.......eee....eeeeee......eeeeeee....eeeeee...............eeehhhhhhhhhhhhh..hhhhhhhh..eee.............eeeeee.....eeeeee....eeee.....ee....hhhhhhhhhhhhh.........eee..eee.....hhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh................eeeeeeeee....eeeeee..eeeeeeee...........eee........ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z71 A   1 GSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTRGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQ 330
                                    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


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333 
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQV 334
               SCOP domains d2z71c_ C: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2z71C00 C:1-331 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) -CBAH-2z71C01 C:2-317                                                                                                                                                                                                                                                                                                        -------------- Pfam domains (1)
           Pfam domains (2) -CBAH-2z71C02 C:2-317                                                                                                                                                                                                                                                                                                        -------------- Pfam domains (2)
         Sec.struct. author .eeeeee.....eeeeeeeee......eeeee.....ee.......ee.....eeeeee......eeeeeee....eeeeee...............eeehhhhhhhhhhhhh.hhhhhhhhh..eee.............eeeeee.....eeeeee....eeee.....ee....hhhhhhhhhhhhh.........eee..eee................hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh................eeeeeeeee....eeeeee......eeee...........eee........ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z71 C   1 GSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTRGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQV 331
                                    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
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (PAC_LYSSH | P12256)
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:0008953    penicillin amidase activity    Catalysis of the reaction: penicillin + H2O = a carboxylate + 6-aminopenicillanate.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAC_LYSSH | P12256: 2iwm 2pva 2quy 3mji 3pva

(-) Related Entries Specified in the PDB File

2iwm 2pva 2quy 3pva