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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX OF THE PEPTIDOGLYCAN GLYCOSYLTRANSFERASE DOMAIN FROM AQUIFEX AEOLICUS AND NERYL MOENOMYCIN A
 
Authors :  Y. Yuan, P. Sliz, S. Walker
Date :  11 May 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptidoglycan Glycosyltransferase, Cell Wall Biosynthesis, Antibiotics, Penicillin-Binding Protein, Transglycosylase, Moenomycin, Antibiotic Resistance, Cell Shape, Cell Wall Biogenesis/Degradation, Hydrolase, Inner Membrane, Membrane, Multifunctional Enzyme, Peptidoglycan Synthesis, Signal-Anchor, Transmembrane, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yuan, S. Fuse, B. Ostash, P. Sliz, D. Kahne, S. Walker
Structural Analysis Of The Contacts Anchoring Moenomycin To Peptidoglycan Glycosyltransferases And Implications For Antibiotic Design.
Acs Chem. Biol. V. 3 429 2008
PubMed-ID: 18642800  |  Reference-DOI: 10.1021/CB800078A

(-) Compounds

Molecule 1 - PENICILLIN-INSENSITIVE TRANSGLYCOSYLASE
    Chains: A
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET48(B)+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MRCA, PONA
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5
    Synonym: PEPTIDOGLYCAN TGASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1M4O1Ligand/Ion(2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-5-{[(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-5-{[(2R,3R,4S,5R,6S)-6-CARBAMOYL-3,4,5-TRIHYDROXYTETRAHYDRO-2H-PYRAN-2-YL]OXY}-4-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-4-HYDROXY-6-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}-6-CARBAMOYL-4-(CARBAMOYLOXY)-5-HYDROXY-5-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-{[(2Z)-3,7-DIMETHYLOCTA-2,6-DIEN-1-YL]OXY}PROPANOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1M4O2Ligand/Ion(2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-5-{[(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-5-{[(2R,3R,4S,5R,6S)-6-CARBAMOYL-3,4,5-TRIHYDROXYTETRAHYDRO-2H-PYRAN-2-YL]OXY}-4-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-4-HYDROXY-6-({[(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}METHYL)TETRAHYDRO-2H-PYRAN-2-YL]OXY}-6-CARBAMOYL-4-(CARBAMOYLOXY)-5-HYDROXY-5-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-{[(2Z)-3,7-DIMETHYLOCTA-2,6-DIEN-1-YL]OXY}PROPANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:83 , GLY A:114 , GLN A:121 , LYS A:124 , ASN A:125 , ARG A:132 , THR A:133 , LEU A:134 , LYS A:137 , ILE A:164 , PRO A:200 , LYS A:201 , PRO A:203 , ALA A:204 , GLU A:238 , ASN A:242 , HOH A:259 , HOH A:284 , HOH A:291BINDING SITE FOR RESIDUE M4O A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D3H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D3H)

(-) Exons   (0, 0)

(no "Exon" information available for 3D3H)

(-) 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:174
 aligned with PBPA_AQUAE | O66874 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:183
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           PBPA_AQUAE    61 QKRFYVSIDKIPEHVINAFVATEDRNFWHHFGIDPVAIVRAAIVNYRAGRIVQGGSTITQQLAKNLFLTRERTLERKIKEALLAIKIERTFDKKKIMELYLNQIYLGSGAYGVEAAAQVYFGKHVWELSLDEAALLAALPKAPAKYNPFYHPERALQRRNLVLKRMLEEGYITPEQYEEAVNK 243
               SCOP domains d3d3ha_ A: Penicillin-binding protein 1a, P         BP1a                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh---------....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3h A  61 QKRFYVSIDKIPEHVINAFVATEDRNFWHHFGIDPVAIVRAAI---------QGGSTITQQLAKNLFLTRERTLERKIKEALLAIKIERTFDKKKIMELYLNQIYLGSGAYGVEAAAQVYFGKHVWELSLDEAALLAALPKAPAKYNPFYHPERALQRRNLVLKRMLEEGYITPEQYEEAVNK 243
                                    70        80        90       100  |      -  |    120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                                    103       113
   Legend:   → Mismatch (orange background)
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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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D3H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D3H)

(-) 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

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        PBPA_AQUAE | O66874: 2oqo 3nb6 3nb7

(-) Related Entries Specified in the PDB File

2oqo