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(-) Description

Title :  STRUCTURE OF A PUTATIVE PEPTIDOGLYCAN GLYCOSYLTRANSFERASE FROM ATOPOBIUM PARVULUM IN COMPLEX WITH PENICILLIN G
 
Authors :  E. V. Filippova, G. Minasov, L. Shuvalova, O. Kiryukhina, G. Babnigg, E J. Sacchettini, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Confe Susceptibility To Known Mtb Inhibitors (Mtbi)
Date :  04 Oct 13  (Deposition) - 30 Oct 13  (Release) - 13 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, Susceptibility To Known Mtb Inhibitors, Mtbi, Glycosyltransferase, Penicillin G, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, G. Minasov, L. Shuvalova, O. Kiryukhina, G. Babnigg, E. Rubin, J. Sacchettini, A. Joachimiak, W. F. Anderson
Structure Of A Putative Peptidoglycan Glycosyltransferase From Atopobium Parvulum In Complex With Penicillin G
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: PENICILLIN-BINDING DOMAIN, UNP RESIDUES 515-954
    Gene: APAR_1344
    Organism Common: STREPTOCOCCUS PARVULUS
    Organism Scientific: ATOPOBIUM PARVULUM
    Organism Taxid: 521095
    Strain: DSM 20469

 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  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MSE26Mod. Amino AcidSELENOMETHIONINE
2PNM2Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2PNM1Ligand/IonOPEN FORM - PENICILLIN G

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:682 , TYR A:720 , SER A:737 , ASN A:739 , THR A:876 , THR A:891 , GLY A:892 , THR A:893 , ASP A:895 , HOH A:1101BINDING SITE FOR RESIDUE PNM A 1001
2AC2SOFTWARESER B:682 , TYR B:720 , SER B:737 , ASN B:739 , THR B:876 , THR B:891 , GLY B:892 , THR B:893 , ASP B:895 , HOH B:1101 , HOH B:1164BINDING SITE FOR RESIDUE PNM B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N1X)

(-) 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 4N1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N1X)

(-) Exons   (0, 0)

(no "Exon" information available for 4N1X)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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....eeeeee...eeeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee.hhh.eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4n1x A 523 SAYVQRGAIITSDGVTLAESVKQDDGTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTDWRSALYSmAGINTTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQA 949
                                   532       542       552      |562       572       582  ||   598 |     608       618       628       638       648       658||     675       685       695       705    |  715       725       735       745       755       765       775  |    785       795       805      |815       825  |    835       845       855       865  |    875  |    885       895       905       915       925       935       945    
                                                              559-MSE              580-MSE5|     600-MSE           618-MSE           636-MSE                659|                                        710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                   
                                                                                         592                                                                 667                                                                                                                  784-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..hhhhhhhhhhhhh..eeeeeee......eeeeeee....hhhhhh..............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh................hhhhhhhhhhhhhh..eee....eeeeee...eeeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee.hhh.eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n1x B 523 SAYQRGAIITSDGVTLAESVKQDDGTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTWRSALYSmAGITGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTISQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQAL 950
                              ||   533       543       553     | 563       573      |583 ||    600  ||   612     | 622       632   |   642       652       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  
                            525|                             559-MSE              580-MSE5|      |  ||         618-MSE           636-MSE                 660|                                        710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                    
                             527                                                        593      |  ||                                                    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 4N1X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N1X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N1X)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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    Gly A:806 - Pro A:807   [ RasMol ]  
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        C8W8H7_ATOPD | C8W8H7: 4jbf 4qjg 4r0q 4r1g 4r23 4r3j 4ra7

(-) Related Entries Specified in the PDB File

4jbf