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(-) Description

Title :  STRUCTURE OF A PUTATIVE PEPTIDOGLYCAN GLYCOSYLTRANSFERASE FROM ATOPOBIUM PARVULUM IN COMPLEX WITH CEPHALOTHIN
 
Authors :  E. V. Filippova, G. Minasov, O. Kiryukhina, S. Clancy, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  01 Aug 14  (Deposition) - 27 Aug 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 (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 Cephalothin
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: UNP 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, 32)

Asymmetric Unit (4, 32)
No.NameCountTypeFull Name
1B3P2Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CEP2Ligand/IonCEPHALOTHIN GROUP
3MSE26Mod. Amino AcidSELENOMETHIONINE
4SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CEP1Ligand/IonCEPHALOTHIN GROUP
3MSE13Mod. Amino AcidSELENOMETHIONINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CEP1Ligand/IonCEPHALOTHIN GROUP
3MSE13Mod. Amino AcidSELENOMETHIONINE
4SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:682 , HIS A:718 , TYR A:720 , SER A:737 , ASN A:739 , LYS A:890 , THR A:891 , GLY A:892 , THR A:893 , ASP A:895 , HOH A:1220 , HOH A:1306BINDING SITE FOR RESIDUE CEP A 1001
2AC2SOFTWAREARG A:759 , GLY A:764 , SER A:776 , LEU A:777 , MSE A:778 , HOH A:1307BINDING SITE FOR RESIDUE SCN A 1002
3AC3SOFTWAREARG A:759 , GLY A:764 , LEU A:777 , PRO A:804 , HOH A:1179BINDING SITE FOR RESIDUE B3P A 1003
4AC4SOFTWARESER B:682 , TYR B:720 , SER B:737 , ASN B:739 , THR B:891 , GLY B:892 , THR B:893 , PHE B:901 , HOH B:1185BINDING SITE FOR RESIDUE CEP B 1001
5AC5SOFTWAREARG B:759 , GLY B:764 , SER B:776 , LEU B:777 , MSE B:778BINDING SITE FOR RESIDUE SCN B 1002
6AC6SOFTWAREASN B:780 , PRO B:804 , HOH B:1153BINDING SITE FOR RESIDUE B3P B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R0Q)

(-) 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 4R0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4R0Q)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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...hhhhhh..............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeeee...eeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r0q A 523 SAYVQRGAIITSDGVTLAESVKQDDGTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTRSALYSmAGINTTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQAL 950
                                   532       542       552      |562       572       582  ||   600       610       620       630     | 640       650       667       677       687       697       707  |    717       727       737       747       757       767       777|     |787       797       807    |  817       827|      837       847       857       867|      877|      887       897       907       917       927       937       947   
                                                              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                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....eeeeeee....eeee......hhhhhheee...eeehhhhhhhhhhh...hhhhh.......eeee..hhhhhhhhhhhh...eeeeeee......eeeeeee...hhhhhh..............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh................hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeeee...eeeeeeeeee......eeeeeeeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r0q B 523 SAYVQRGAIITSDGVTLAESVKQDDTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTRSALYSmAGINTTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQAL 950
                                   532       542    || 553     | 563       573      |583 ||    601       611      |621       631    |  641       651       668       678       688       698       708 |     718      |728       738       748       758       768       778     | 788       798       808   |   818       828       838       848       858       868       878       888       898       908       918       928       938       948  
                                                  547|       559-MSE              580-MSE5|     |               618-MSE           636-MSE                659|                                        710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                    
                                                   549                                  594     |                                                         667                                                                                                                  784-MSE                                                                                                                                                                  
                                                                                              600-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 4R0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R0Q)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        C8W8H7_ATOPD | C8W8H7: 4jbf 4n1x 4qjg 4r1g 4r23 4r3j 4ra7

(-) Related Entries Specified in the PDB File

4jbf
4n1x
4qjg
4r1g RELATED ID: MCSG-APC110119 RELATED DB: TARGETTRACK