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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FULL-LENGTH TRANSGLYCOSYLASE PBP1B FROM ESCHERICHIA COLI
 
Authors :  M. T. Sung, Y. T. Lai, C. Y. Huang, L. Y. Chou, C. H. Wong, C. Ma
Date :  19 Jan 09  (Deposition) - 02 Jun 09  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacterial Cell Wall Synthesis, Penicillin-Binding Protein, Antibiotics Design, Alternative Initiation, Antibiotic Resistance, Cell Inner Membrane, Cell Membrane, Cell Shape, Cell Wall Biogenesis/Degradation, Glycosyltransferase, Hydrolase, Membrane, Multifunctional Enzyme, Peptidoglycan Synthesis, Signal-Anchor, Transferase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. T. Sung, Y. T. Lai, C. Y. Huang, L. Y. Chou, H. W. Shih, W. C. Cheng, C. H. Wong, C. Ma
Crystal Structure Of The Membrane-Bound Bifunctional Transglycosylase Pbp1B From Escherichia Coli.
Proc. Natl. Acad. Sci. Usa V. 106 8824 2009
PubMed-ID: 19458048  |  Reference-DOI: 10.1073/PNAS.0904030106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
    ChainsA
    EC Number2.4.1.129, 3.4.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 54-804
    GeneB0149, JW0145, MRCB, PBPF, PONB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainK-12
    SynonymPBP-1B, PBP1B, MUREIN POLYMERASE, PENICILLIN- INSENSITIVE TRANSGLYCOSYLASE, PEPTIDOGLYCAN GLYCOSYLTRANSFERASE, PEPTIDOGLYCAN TGASE, PENICILLIN- SENSITIVE TRANSPEPTIDASE, DD-TRANSPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric/Biological Unit (2, 25)
No.NameCountTypeFull Name
1M0E1Ligand/IonMOENOMYCIN
2MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:233 , GLN A:271 , LYS A:274 , ARG A:286 , GLN A:318 , GLU A:323 , VAL A:354 , LYS A:355 , GLY A:356 , ALA A:357 , SER A:358 , ILE A:359BINDING SITE FOR RESIDUE M0E A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:280 -Glu A:281
2Ser A:283 -Tyr A:284
3Gln A:382 -Gln A:383
4Gln A:523 -Pro A:524

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FWL)

(-) 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:707
 aligned with PBPB_ECOLI | P02919 from UniProtKB/Swiss-Prot  Length:844

    Alignment length:734
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       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       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795    
           PBPB_ECOLI    66 LWLLLKLAIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRMVNLEPDMTISKNEMVKLLEATQYRQVSKMTRPGEFTVQANSIEMIRRPFDFPDSKEGQVRARLTFDGDHLATIVNMENNRQFGFFRLDPRLITMISSPNGEQRLFVPRSGFPDLLVDTLLATEDRHFYEHDGISLYSIGRAVLANLTAGRTVQGASTLTQQLVKNLFLSSERSYWRKANEAYMALIMDARYSKDRILELYMNEVYLGQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGMVKGASIYNPWRNPKLALERRNLVLRLLQQQQIIDQELYDMLSARPLGVQPRGGVISPQPAFMQLVRQELQAKLGDKVKDLSGVKIFTTFDSVAQDAAEKAAVEGIPALKKQRKLSDLETAIVVVDRFSGEVRAMVGGSEPQFAGYNRAMQARRSIGSLAKPATYLTALSQPKIYRLNTWIADAPIALRQPNGQVWSPQNDDRRYSESGRVMLVDALTRSMNVPTVNLGMALGLPAVTETWIKLGVPKDQLHPVPAMLLGALNLTPIEVAQAFQTIASGGNRAPLSALRSVIAEDGKVLYQSFPQAERAVPAQAAYLTLWTMQQVVQRGTGRQLGAKYPNLHLAGKTGTTNNNVDTWFAGIDGSTVTITWVGRDNNQPTKLYGASGAMSIYQRYLANQTPTPLNLVPPEDIADMGVDYDGNFVCSGGMRILPVWTSDPQSLCQQSEM 799
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fwlA01 A:66-96                ------3fwlA02-3fwlA03 A:111-200 Penicillin-binding protein 1b domain                                    3fwlA04 A:201-397 Penicillin binding protein tra                   nspeptidase domain                                                                                                                3        fwlA02 A:103-109,A:398-798 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhhhhh...hhhhhh........eee....ee......hhhhhhhhhhhh..ee........eeee...eeeeee............eeeeeeee..eeeeeee....ee...ee....eeee......ee....hhhhhhhhhhhhhhh........hhhhh....-------------------.....hhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhh...eeee....eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh....................--------....hhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeee.................ee.hhhhhhhhhhhhhh.........eee.....ee.....ee.............eeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhh..eehhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhh..hhhhhhhh.....eeeee.hhhh.eeeeeee...eeeeeeee...........hhhhhhhhhhhhhhh............eeeeee.....ee.....eeeeee....hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwl A  66 LWLLLKLAIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRmVNLEPDmTISKNEmVKLLEATQYRQVSKmTRPGEFTVQANSIEmIRRPFDFPDSKEGQVRARLTFDGDHLATIVNmENNRQFGFFRLDPRLITmISSPNGEQRLFVPRSGFPDLLVDTLLATEDRHFYEHDGISLYSI-------------------LTQQLVKNLFLSSERSYWRKANEAYmALImDARYSKDRILELYmNEVYLGQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGmVKGASIYNPWRNPKLALERRNLVLRLLQQQQIIDQELYDmLSARP--------VISPQPAFmQLVRQELQAKLGDKVKDLSGVKIFTTFDSVAQDAAEKAAVEGIPALKKQRKLSDLETAIVVVDRFSGEVRAmVGGSEPQFAGYNRAmQARRSIGSLAKPATYLTALSQPKIYRLNTWIADAPIALRQPNGQVWSPQNDDRRYSESGRVmLVDALTRSmNVPTVNLGmALGLPAVTETWIKLGVPKDQLHPVPAmLLGALNLTPIEVAQAFQTIASGGNRAPLSALRSVIAEDGKVLYQSFPQAERAVPAQAAYLTLWTmQQVVQRGTGRQLGAKYPNLHLAGKTGTTNNNVDTWFAGIDGSTVTITWVGRDNNQPTKLYGASGAmSIYQRYLANQTPTPLNLVPPEDIADmGVDYDGNFVCSGGmRILPVWTSDPQSLCQQSEm 799
                                    75        85        95       105    |  115 |     125       135   |   145       155       165       175       185|      195       205       215       225       235       245  |      -         -  |    275       285       295 |     305     | 315       325       335       345       355       365       375       385       395  |      - |     415       425       435       445       455       465       475       485 |     495      |505       515       525       535       545       555       565       575      |585       595       605   |   615       625       635       645       655       665       675       685       695       705       715       725       735    |  745       755       765|      775    |  785       795   |
                                                                      110-MSE  |      |            139-MSE        154-MSE                         186-MSE           204-MSE                                     248                 268                      293-MSE           311-MSE                                   353-MSE                                 393-MSE8      407     415-MSE                                                                 487-MSE        502-MSE                                                       564-MSE  573-MSE  582-MSE                    609-MSE                                                          674-MSE                                                           740-MSE                   766-MSE       780-MSE            799-MSE
                                                                             117-MSE  |                                                                                                                                                                          297-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                    124-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

   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  (0, 0)

(no "SCOP Domain" information available for 3FWL)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PBPB_ECOLI | P02919)
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:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008955    peptidoglycan glycosyltransferase activity    Catalysis of the reaction: [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-diphosphoundecaprenol + GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0071575    integral component of external side of plasma membrane    The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane.
    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:0009274    peptidoglycan-based cell wall    A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli.
    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)

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        PBPB_ECOLI | P029193vma 5fgz 5hl9 5hla 5hlb 5hld

(-) Related Entries Specified in the PDB File

3fwm