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(-) Description

Title :  STRUCTURE OF A PUTATIVE PEPTIDOGLYCAN GLYCOSYLTRANSFERASE FROM ATOPOBIUM PARVULUM IN COMPLEX WITH CEFAPIRIN
 
Authors :  E. V. Filippova, G. Minasov, O. Kiryukhina, S. Clancy, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  15 Aug 14  (Deposition) - 17 Sep 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
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 Cefapirin
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 Common: STREPTOCOCCUS PARVULUS
    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
1CFU2Ligand/Ion(2R)-2-[(1R)-1-(ACETYLAMINO)-2-OXOETHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2GOL3Ligand/IonGLYCEROL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1CFU1Ligand/Ion(2R)-2-[(1R)-1-(ACETYLAMINO)-2-OXOETHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1CFU1Ligand/Ion(2R)-2-[(1R)-1-(ACETYLAMINO)-2-OXOETHYL]-5-METHYL-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:682 , TYR A:720 , SER A:737 , ASN A:739 , THR A:876 , LYS A:890 , THR A:891 , GLY A:892 , THR A:893BINDING SITE FOR RESIDUE CFU A 1001
2AC2SOFTWARETYR A:554 , HIS A:556 , ASP A:557 , GLY A:558 , MSE A:559 , SER A:561 , GLY A:565BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWARESER A:568 , THR A:569 , GLN A:570BINDING SITE FOR RESIDUE PO4 A 1003
4AC4SOFTWAREGLN A:854 , SER A:857 , ALA A:858 , HOH A:1191BINDING SITE FOR RESIDUE PO4 A 1004
5AC5SOFTWAREGLY B:681 , SER B:682 , TYR B:720 , SER B:737 , ASN B:739 , THR B:876 , LYS B:890 , THR B:891 , GLY B:892 , THR B:893BINDING SITE FOR RESIDUE CFU B 1001
6AC6SOFTWARETYR B:554 , ASP B:557 , GLY B:558 , MSE B:559 , SER B:561 , GLY B:565 , TYR B:652BINDING SITE FOR RESIDUE GOL B 1002
7AC7SOFTWARETYR B:571 , HIS B:654 , ALA B:655 , LEU B:657 , GLY B:658 , PO4 B:1004BINDING SITE FOR RESIDUE GOL B 1003
8AC8SOFTWARESER B:568 , THR B:569 , GLN B:570 , GOL B:1003BINDING SITE FOR RESIDUE PO4 B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3J)

(-) 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 4R3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3J)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3J)

(-) 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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeee....eeee......hhhhhheee...eeehhhhhhhhhhhh...eeee..hhhhhhhhhhhhh..eeeeeee......eeeeeee...hhhhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eee...eeee..eeee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh................hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeee.....eeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3j A 526 VQRGAIITSDGVTLAESVKQDDTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTGTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTIIESGTGSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADNGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQALGAAS 954
                                   535       545 ||    556  |    566       576   |   586|      615  |    625       635|      645       655       665       675       685       695       705    |  715       725       735       745       755       765       775  |    785       795       805      |815       825  |    835       845       855       865  |    875  |    885       895|      907       917       927       937       947       
                                               547|       559-MSE              580-MSE86|         618-MSE           636-MSE                                                                   710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE          895|                                                        
                                                549                                   606                                                                                                                                                                               784-MSE                                                                                                         898                                                        


Chain B from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeee....eeee......hhhhhheee...eeehhhhhhhhhhh...eeee..hhhhhhhhhhhh....eeeeee......eeeeeee...hhhhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eee...eee....eee.hhhh...eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..eee....eeeee.....eeee....eeee..hhhhhhhhhhhhhhhhhhh.hhhhh......eeeeeeee.hhh.eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3j B 526 VQRGAIITSDGVTLAESVKQDDTYVRNYPHDGmASHTVGYISTQYGTAGIESSmNETLTTGSSVVLTINSQmQAVAEAALQGYSGSIVVmDPSTGAVLAKASSPSYTHAELGTIIESGTGSQLVDRTTQALYSPGSSFKTVTLAAGIDTHKTTLDTTYSAPGTmEIGGGTIHNYANEDmGTIPLREAFARSSNTALAQLGVALGADNLVSYARAFGYGTALGQDFSTTPSLmPNPAEmTTWELAWASCGLPVGEHASPAGPQTTVmQNAVIAAAIANGGVVmNPYIVDRVLSPEGAVVSTTSPKSLGQAVSADTAAQVREAmLGVVESGTGmGARVPGVKIAGKTGTADVENGNFNSFFIGFAPYDHPTLVVSVVIEGNGENVLGYGAQVGGRVLAQCLNIQALGAA 953
                                   535       545 ||    556  |    566       576   |   606       616 |     626       636       646       656       666       676       686       696       706   |   716       726       736       746       756       766       776 |     786       796       806     | 816       826 |     836       846       856       866 |     876 |     886       896       906       916       926       936       946       
                                               547|       559-MSE              580-MSE5|         618-MSE           636-MSE                                                                   710-MSE        725-MSE                                              778-MSE |                         812-MSE         828-MSE                                 868-MSE   878-MSE                                                                       
                                                549                                  606                                                                                                                                                                               784-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 4R3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3J)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        C8W8H7_ATOPD | C8W8H7: 4jbf 4n1x 4qjg 4r0q 4r1g 4r23 4ra7

(-) Related Entries Specified in the PDB File

4jbf
4n1x
4qjg
4r0q
4r1g
4r23 RELATED ID: MCSG-APC110119 RELATED DB: TARGETTRACK