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(-) Description

Title :  CRYSTAL STRUCTURE OF PBP1A FROM DRUG-RESISTANT STRAIN 5204 FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  V. Job, R. Carapito, T. Vernet, O. Dideberg, A. Dessen, A. Zapun
Date :  05 Jun 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,F
Keywords :  Transpeptidase Activity, Peptidoglycan Synthesis, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Job, R. Carapito, T. Vernet, A. Dessen, A. Zapun
Common Alterations In Pbp1A From Resistant Streptococcus Pneumoniae Decrease Its Reactivity Toward {Beta}-Lactams: Structural Insights.
J. Biol. Chem. V. 283 4886 2008
PubMed-ID: 18055459  |  Reference-DOI: 10.1074/JBC.M706181200

(-) Compounds

Molecule 1 - PENICILLIN BINDING PROTEIN 1A
    Chains: A
    EC Number: 2.4.1.129
    Engineered: YES
    Fragment: GLYCOSYLTRASFERASE DOMAIN, RESIDUES 47-70
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 5204
 
Molecule 2 - PENICILLIN BINDING PROTEIN 1A
    Chains: F
    EC Number: 3.4.16.4
    Engineered: YES
    Fragment: TRANSPEPTIDASE DOMAIN, GLYCOSYLTRASFERASE DOMAIN, RESIDUES 264-653
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 5204

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BA1Ligand/IonBARIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR F:364 , SER F:472 , ASN F:473 , TYR F:476 , HOH F:2059 , HOH F:2118 , HOH F:2119BINDING SITE FOR RESIDUE BA F1652
2AC2SOFTWARESER F:370 , TRP F:411 , PHE F:416 , SER F:428 , THR F:543 , THR F:558 , GLY F:559 , THR F:560 , GLU F:582 , HOH F:2194BINDING SITE FOR RESIDUE MES F1653

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V2F)

(-) Exons   (0, 0)

(no "Exon" information available for 2V2F)

(-) 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
                                    61      
           PBPA_STRR6    52 SSKIYDNKNQLIADLG  67
               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
                 2v2f A  52 SSKIYDNKNQLIADLG  67
                                    61      


Chain A from PDB  Type:PROTEIN  Length:16
 aligned with Q9RET4_STREE | Q9RET4 from UniProtKB/TrEMBL  Length:719

    Alignment length:16
                                    61      
         Q9RET4_STREE    52 SSKIYDNKNQLIADLG  67
               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
                 2v2f A  52 SSKIYDNKNQLIADLG  67
                                    61      


Chain F from PDB  Type:PROTEIN  Length:367
 aligned with Q9RET4_STREE | Q9RET4 from UniProtKB/TrEMBL  Length:719

    Alignment length:384
                                   277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647    
         Q9RET4_STREE   268 YPAYMDNYLKEVINQVEQETGYNLLTTGMDVYTNVDQEAQKHLWDIYNSDQYVSYPDDDLQVASTVVDVSNGKVIAQLGARHQASNVSFGTNQAVETNRDWGSAMKPITDYAPAIEYGVYDSTATMVNDIPYNYPGTSTPVYNWDRAYFGNITLQYALQQSRNVTAVETLNKVGLDRAKTFLNGLGIDYPSMHYANAISSNTTESNKQYGASSEKMAAAYAAFANGGIYHKPMYINKVVFSDGSKKEFSDVGTRAMKETTAYMMTEMMKTVLAYGTGRGAYLPWLAQAGKTGTSNYTDDEIEKHIKNTGYVAPDEMFVGYTRKYSMAVWTGYSNRLTPIVGDGFLVAAKVYRSMITYLSEGSNPEDWNIPEGLYRNGEFVFKNG 651
               SCOP domains d2v2ff_ F: automated matches                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...........eeeeeeee.....eeeee....-----.............hhhhhhhhhhhhhhhhh........eeee..ee......ee........eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.............hhhhhhhhhhhhhh..ee.....eeeeee....eee.....ee..hhhhhhhhhhhhhhhhhh..hhhhh......eeeeee.....-----------....eeeeeee...eeeeeeee........hhhhhhhhhhhhhhhhhhhhh..-.........eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v2f F 268 YPAYMDNYLKEVINQVEQETGYNLLTTGMDVYTNVDQEAQKHLWDIYNSDQYVSYPDDDLQVASTVVDVSNGKVIAQLGARH-----SFGTNQAVETNRDWGSAMKPITDYAPAIEYGVYDSTATMVNDIPYNYPGTSTPVYNWDRAYFGNITLQYALQQSRNVTAVETLNKVGLDRAKTFLNGLGIDYPSMHYANAISSNTTESNKQYGASSEKMAAAYAAFANGGIYHKPMYINKVVFSDGSKKEFSDVGTRAMKETTAYMMTEMMKTVLAYGTGRGAYLPWLAQAGKTGTSNYTD-----------YVAPDEMFVGYTRKYSMAVWTGYSNRLTPIVGDGFLVAAKVYRSMITYLSEGS-PEDWNIPEGLYRNGEFVFKNG 651
                                   277       287       297       307       317       327       337       347 |     357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       | -       577       587       597       607       617       627 | |   637       647    
                                                                                                           349   355                                                                                                                                                                                                               565         577                                                 629 |                    
                                                                                                                                                                                                                                                                                                                                                                                                     631
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2V2F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V2F)

(-) Gene Ontology  (10, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain A,F   (Q9RET4_STREE | Q9RET4)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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        PBPA_STRR6 | Q8DR59: 2c5w 2c6w 2zc5 2zc6

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