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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS PEPTIDOGLYCAN GLYCOSYLTRANSFERASE IN COMPLEX WITH DECARBOXYLATED NERYL MOENOMYCIN
 
Authors :  P. Sliz, Y. Yuan, S. Walker
Date :  02 Jun 10  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycosyltransferases, Peptidoglycan Glycosyltransferase, Polysaccharides, Cell Wall, Antibiotics, Moenomycin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Fuse, H. Tsukamoto, Y. Yuan, T. S. Wang, Y. Zhang, M. Bolla, S. Walker P. Sliz, D. Kahne
Functional And Structural Analysis Of A Key Region Of The Cell Wall Inhibitor Moenomycin.
Acs Chem. Biol. V. 5 701 2010
PubMed-ID: 20496948  |  Reference-DOI: 10.1021/CB100048Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1A
    ChainsA
    EC Number2.4.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET48 B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 59-243
    GeneAQ_624, MRCA, PONA
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
    StrainVF5
    SynonymPBP-1A, PBP1A, PENICILLIN-INSENSITIVE TRANSGLYCOSYLASE, PEPTIDOGLYCAN TGASE, PENICILLIN-SENSITIVE TRANSPEPTIDASE, DD- TRANSPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NB7)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

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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:177
 aligned with PBPA_AQUAE | O66874 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:185
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238     
           PBPA_AQUAE    59 GIQKRFYVSIDKIPEHVINAFVATEDRNFWHHFGIDPVAIVRAAIVNYRAGRIVQGGSTITQQLAKNLFLTRERTLERKIKEALLAIKIERTFDKKKIMELYLNQIYLGSGAYGVEAAAQVYFGKHVWELSLDEAALLAALPKAPAKYNPFYHPERALQRRNLVLKRMLEEGYITPEQYEEAVNK 243
               SCOP domains d3nb7a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Transgly-3nb7A01 A:59-227                                                                                                                                                ---------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh--------....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb7 A  59 GIQKRFYVSIDKIPEHVINAFVATEDRNFWHHFGIDPVAIVRAAIV--------QGGSTITQQLAKNLFLTRERTLERKIKEALLAIKIERTFDKKKIMELYLNQIYLGSGAYGVEAAAQVYFGKHVWELSLDEAALLAALPKAPAKYNPFYHPERALQRRNLVLKRMLEEGYITPEQYEEAVNK 243
                                    68        78        88        98     |   -    |  118       128       138       148       158       168       178       188       198       208       218       228       238     
                                                                       104      113                                                                                                                                  

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  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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NB7)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (PBPA_AQUAE | O66874)
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: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:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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: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
        PBPA_AQUAE | O668742oqo 3d3h 3nb6

(-) Related Entries Specified in the PDB File

2oqo 3d3h 3nb6