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(-) Description

Title :  STRUCTURE OF A PUTATIVE PEPTIDOGLYCAN GLYCOSYLTRANSFERASE FROM ATOPOBIUM PARVULUM IN COMPLEX WITH DICLOXACILLIN
 
Authors :  E. V. Filippova, G. Minasov, O. Kiryukhina, S. Clancy, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  08 Aug 14  (Deposition) - 17 Sep 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Penicillin-Binding Protein, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, G. Minasov, O. Kiryukhina, S. Clancy, A. Joachimiak, W. F. Anderson
Structure Of A Putative Peptidoglycan Glycosyltransferase From Atopobium Parvulum In Complex With Dicloxacillin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN GLYCOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.1.129
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 505-954
    Gene: APAR_1344
    Organism Scientific: ATOPOBIUM PARVULUM DSM 20469
    Organism Taxid: 521095
    Strain: ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 37)

Asymmetric Unit (4, 37)
No.NameCountTypeFull Name
1DXU2Ligand/Ion(3R,4R,5R)-3-(2,6-DICHLOROPHENYL)-N-{(1R)-1-[(2R,4S)-4-(DIHYDROXYMETHYL)-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL]-2-OXOETHYL}-5-METHYL-1,2-OXAZOLIDINE-4-CARBOXAMIDE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE26Mod. Amino AcidSELENOMETHIONINE
4P4G4Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Biological Unit 1 (4, 20)
No.NameCountTypeFull Name
1DXU1Ligand/Ion(3R,4R,5R)-3-(2,6-DICHLOROPHENYL)-N-{(1R)-1-[(2R,4S)-4-(DIHYDROXYMETHYL)-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL]-2-OXOETHYL}-5-METHYL-1,2-OXAZOLIDINE-4-CARBOXAMIDE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE13Mod. Amino AcidSELENOMETHIONINE
4P4G3Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Biological Unit 2 (4, 17)
No.NameCountTypeFull Name
1DXU1Ligand/Ion(3R,4R,5R)-3-(2,6-DICHLOROPHENYL)-N-{(1R)-1-[(2R,4S)-4-(DIHYDROXYMETHYL)-5,5-DIMETHYL-1,3-THIAZOLIDIN-2-YL]-2-OXOETHYL}-5-METHYL-1,2-OXAZOLIDINE-4-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE13Mod. Amino AcidSELENOMETHIONINE
4P4G1Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:681 , SER A:682 , HIS A:718 , TYR A:720 , SER A:737 , ASN A:739 , TRP A:791 , CYS A:794 , LEU A:796 , LYS A:890 , THR A:891 , GLY A:892 , THR A:893 , ALA A:894 , ASP A:895 , HOH A:1172BINDING SITE FOR RESIDUE DXU A 1001
2AC2SOFTWARETHR A:699 , ASP A:701 , THR A:702 , HOH A:1144 , HOH A:1266BINDING SITE FOR RESIDUE P4G A 1002
3AC3SOFTWARESER A:579 , GLY A:768 , GLN A:769 , PHE A:771 , HOH A:1307BINDING SITE FOR RESIDUE P4G A 1003
4AC4SOFTWAREGLN A:627 , GLY A:628 , TYR A:629 , SER A:630 , SER A:649 , HOH A:1206BINDING SITE FOR RESIDUE P4G A 1004
5AC5SOFTWAREGLN A:943BINDING SITE FOR RESIDUE EDO A 1006
6AC6SOFTWAREGLY B:681 , SER B:682 , HIS B:718 , TYR B:720 , SER B:737 , ASN B:739 , TRP B:791 , CYS B:794 , THR B:876 , THR B:891 , GLY B:892 , THR B:893 , ASP B:895 , HOH B:1139BINDING SITE FOR RESIDUE DXU B 1001
7AC7SOFTWAREGLY B:768 , GLN B:769BINDING SITE FOR RESIDUE P4G B 1002
8AC8SOFTWARESER B:756 , ALA B:855 , HOH B:1234BINDING SITE FOR RESIDUE EDO B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R23)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:649 -Pro A:650
2Gly A:806 -Pro A:807
3Ala A:909 -Pro A:910
4Ser B:649 -Pro B:650
5Gly B:806 -Pro B:807
6Ala B:909 -Pro B:910

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R23)

(-) Exons   (0, 0)

(no "Exon" information available for 4R23)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....ee.....eeeeeee.....eeee......hhhhhheee...eeehhhhhhhhhhhh....hhhhh......eeee..hhhhhhhhhhhhh..eeeeeee......eeeeeee....hhhhhh..............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee.hhh.eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r23 A 522 KSAYVQRGAIITSDGVTLAESVKQDDGTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTGHRSALYSmAGITTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTISQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQAL 950
                                   531       541       551       561       571       581     ||597  |  ||608       618       628       638       648       658 ||    674       684       694       704     | 714       724|      734       744       754       764       774   |   784       794       804       814       824   |   834       844       854       864   |   874   |   884       894       904       914       924       934       944      
                                                               559-MSE              580-MSE587|     |  ||          618-MSE           636-MSE                 660|                                        710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                    
                                                                                            594     |  ||                                                     667                                                                                                                  784-MSE                                                                                                                                                                  
                                                                                                  600-MSE                                                                                                                                                                                                                                                                                                                                                   
                                                                                                     603|                                                                                                                                                                                                                                                                                                                                                   
                                                                                                      605                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....eeeeeee.....eeee......hhhhhheee...eeehhhhhhhhhhh...hhhhh.....eeee..hhhhhhhhhhhhh..eeeeeee......eeeeeee...hhhhhhh.............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh................hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee.hhh.eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r23 B 523 SAYVQRGAIITSDGVTLAESVKQDDGTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTRSALYSmAGITGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQAL 950
                                   532       542       552      |562       572       582  ||   600  ||   612     | 622       632   |   642       652      |669       679       689       699       709|      719     | 729       739       749       759       769       779    |  789       799       809  |    819       829       839       849       859       869       879       889       899       909       919       929       939       949 
                                                              559-MSE              580-MSE5|     |  ||         618-MSE           636-MSE                659|                                        710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                    
                                                                                         594     |  ||                                                   667                                                                                                                  784-MSE                                                                                                                                                                  
                                                                                               600-MSE                                                                                                                                                                                                                                                                                                                                                 
                                                                                                  603|                                                                                                                                                                                                                                                                                                                                                 
                                                                                                   606
   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 4R23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R23)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        C8W8H7_ATOPD | C8W8H7: 4jbf 4n1x 4qjg 4r0q 4r1g 4r3j 4ra7

(-) Related Entries Specified in the PDB File

4jbf 4n1x 4r0q 4r1g