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(-) Description

Title :  PENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX (CEFOTAXIME) FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  C. Contreras-Martel, V. Job, A. -M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen
Date :  02 Nov 05  (Deposition) - 07 Dec 05  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peptidoglycan Synthesis, Transferase-Hydrolase Complex, Antibiotic Resistance, Cell Shape, Multifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contreras-Martel, V. Job, A. -M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen
Crystal Structure Of Penicillin-Binding Protein 1A (Pbp1A) Reveals A Mutational Hotspot Implicated In Beta-Lactam Resistance In Streptococcus Pneumoniae.
J. Mol. Biol. V. 355 684 2006
PubMed-ID: 16316661  |  Reference-DOI: 10.1016/J.JMB.2005.10.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJAH143
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GLYLOSYLTRANSFERASE DOMAIN, RESIDUES 51-66
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: PBP-1A, EXPORTED PROTEIN 2
 
Molecule 2 - PENICILLIN-BINDING PROTEIN 1A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJAH143
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 267-650
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: PBP-1A, EXPORTED PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PCZ1Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-METHYLIDENE-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
4ZN5Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:309 , GLU B:514 , HOH B:2040 , HOH B:2063BINDING SITE FOR RESIDUE ZN B 701
02AC2SOFTWAREHIS B:395 , GLU B:397 , GLU B:435BINDING SITE FOR RESIDUE ZN B 702
03AC3SOFTWAREHIS B:460 , GLU B:566 , HIS B:571 , HOH B:2064BINDING SITE FOR RESIDUE ZN B 703
04AC4SOFTWAREGLU B:318 , HIS B:503BINDING SITE FOR RESIDUE ZN B 704
05AC5SOFTWAREHIS B:349BINDING SITE FOR RESIDUE ZN B 705
06AC6SOFTWAREILE B:393 , ASN B:418BINDING SITE FOR RESIDUE CL B 706
07AC7SOFTWAREASP B:297 , GLU B:638BINDING SITE FOR RESIDUE CL B 707
08AC8SOFTWARESER B:462 , ASN B:562 , EDO B:712BINDING SITE FOR RESIDUE EDO B 711
09AC9SOFTWARETYR B:409 , ASN B:410 , TRP B:411 , EDO B:711 , PCZ B:1370BINDING SITE FOR RESIDUE EDO B 712
10BC1SOFTWAREASP B:367 , SER B:370 , TRP B:411 , SER B:428 , ASN B:430 , ILE B:465 , THR B:558 , GLY B:559 , THR B:560 , SER B:561 , ASN B:562 , EDO B:712BINDING SITE FOR RESIDUE PCZ B1370

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C5W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C5W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C5W)

(-) Exons   (0, 0)

(no "Exon" information available for 2C5W)

(-) 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:16
 aligned with PBPA_STRR6 | Q8DR59 from UniProtKB/Swiss-Prot  Length:719

    Alignment length:16
                                    60      
           PBPA_STRR6    51 TSSKIYDNKNQLIADL  66
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...eee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2c5w A  51 TSSKIYDNKNQLIADL  66
                                    60      


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with PBPA_STRR6 | Q8DR59 from UniProtKB/Swiss-Prot  Length:719

    Alignment length:385
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645     
           PBPA_STRR6   266 SNYPAYMDNYLKEVINQVEEETGYNLLTTGMDVYTNVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQAVETNRDWGSTMKPITDYAPALEYGVYESTATIVHDEPYNYPGTNTPVYNWDRGYFGNITLQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLSYGTGRNAYLAWLPQAGKTGTSNYTDEEIENHIKTSQFVAPDELFAGYTRKYSMAVWTGYSNRLTPLVGNGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKN 650
               SCOP domains d2c5wb1 B:266-650 Penicillin-binding protein 1a, transpeptidase domain                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...........eeeeeeee.....eeeee......................hhhhhhhhhhhhhhhhh........eeee....................eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.............hhhhhhhhhhhhhh..eee....eeeeee....eee....eee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeee...hhhhhhhh......ee..eeeeee...eeeeeeee.......ee.hhhhhhhhhhhhhhhhhhh............eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c5w B 266 SNYPAYMDNYLKEVINQVEEETGYNLLTTGMDVYTNVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQAVETNRDWGSTMKPITDYAPALEYGVYESTATIVHDEPYNYPGTNTPVYNWDRGYFGNITLQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLTYGTGRNAYLAWLPQAGKTGTSNYTDEEIENHIKTSQFVAPDELFAGYTRKYSMAVWTGYSNRLTPLVGNGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKN 650
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C5W)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PBPA_STRR6 | Q8DR59)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PBPA_STRR6 | Q8DR59: 2c6w 2v2f 2zc5 2zc6

(-) Related Entries Specified in the PDB File

2c6w PENICILLIN-BINDING PROTEIN 1A (PBP-1A) FROM STREPTOCOCCUS PNEUMONIAE