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(-) Description

Title :  PENICILLIN-BINDING PROTEIN 2X (PBP-2X) ACYL-ENZYME COMPLEX
 
Authors :  E. J. Gordon, N. Mouz, E. Duee, O. Dideberg
Date :  28 Sep 99  (Deposition) - 25 May 00  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan Synthesis, Cell Wall, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Gordon, N. Mouz, E. Duee, O. Dideberg
The Crystal Structure Of The Penicillin Binding Protein 2X From Streptococcus Pneumoniae And Its Acyl-Enzyme Form: Implication In Drug Resistance
J. Mol. Biol. V. 299 501 2000
PubMed-ID: 10860753  |  Reference-DOI: 10.1006/JMBI.2000.3740
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2X
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PBP2X
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Other Details: COMPLEXED WITH CEFUROXIME ANTIBIOTIC
    Strain: MC1061
    Synonym: PBP-2X, PBP2X

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CES1Ligand/Ion2-[CARBOXY-(2-FURAN-2-YL-2-METHOXYIMINO-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
2KEF1Ligand/IonCEFUROXIME (OCT-3-ENE FORM)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:423 , PRO A:424 , ARG A:426 , VAL A:662 , HOH A:2057BINDING SITE FOR RESIDUE KEF A 900
2AC2SOFTWAREGLU A:334 , SER A:337 , TRP A:374 , SER A:395 , ASN A:397 , PHE A:450 , GLN A:452 , SER A:548 , GLY A:549 , THR A:550 , GLN A:552BINDING SITE FOR LIGAND CES A 800 BOUND TO SER A 337

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:307 -Pro A:308
2Ser A:576 -Pro A:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRPN632-691
692-750		  2A:633-691
A:692-750

(-) Exons   (0, 0)

(no "Exon" information available for 1QMF)

(-) 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:559
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:680
                                    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       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750
           PBPX_STRPN    71 TVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d1qmfa3 A:71-263 Penic                                                                                          illin-binding protein 2x (pbp-2x), N-terminal domain                             d1qmfa4 A:264-620 Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                  d1qmfa1 A:633-692                                           d1qmfa2 A:693-750                                          SCOP domains
               CATH domains 1qmfA01                                                                                                         1qmfA01 A:71-92,A:183-263,A:481-494 Penicillin-bindi                   ng protein1qmfA02 A:264-480,A:495-620 DD-peptidase/beta-lactamase superfamily                                                                                                                                                      1qmfA01       1qmfA02 A:264-480,A:495-620 DD-peptidase/beta-lactamase superfamily                                                                       ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PBP_dimer-1qmfA03 A:71                                                                                          -234                                                                   -----------------------------------Transpeptidase-1qmfA01 A:289-609                                                                                                                                                                                                                                                                                                 -----------            -------------------------------------------------------------PASTA-1qmfA02 A:694-750                                   Pfam domains
         Sec.struct. author ........ee.....eeeeee.------------------------------------------------------------------------------------------..eee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhh.....-------------------......eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhh.......eee...ee....ee.hhhhhh......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhh.....hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..------------............hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhh..eeeee....eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PASTA  PDB: A:633-691 UniProt: 632-691                      PASTA  PDB: A:692-750 UniProt: 692-750                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmf A  71 TVPAKRGTIYDRNGVPIAEDAT------------------------------------------------------------------------------------------SPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGII-------------------RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL------------QSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                    80        90 |       -         -         -         -         -         -         -         -         -  |    190       200       210       220       230   |     -         -   |   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       560       570       580       590       600       610       620         -  |    640       650       660       670       680       690       700       710       720       730       740       750
                                                92                                                                                        183                                                234                 254                                                                                                                                                                                                                                                                                                                                                                           620          633
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)
(-)
Clan: no clan defined [family: PASTA] (12)
(-)
Clan: no clan defined [family: PBP_dimer] (15)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PBPX_STRPN | P14677)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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: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: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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PBPX_STRPN | P14677: 1pmd 1qme 1rp5 2z2l 2z2m 2zc3 2zc4

(-) Related Entries Specified in the PDB File

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