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(-) Description

Title :  CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-RNA CONJUGATE
 
Authors :  I. Li De La Sierra-Gallay, M. Fonvielle, H. Van Tilbeurgh, M. Arthu M. Etheve-Quelquejeu
Date :  20 Dec 12  (Deposition) - 03 Jul 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Femx, Peptidoglycan, Transferase, Peptidyl-Rna Conjugate Complex, Transferase-Peptide-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Fonvielle, I. Li De La Sierra-Gallay, A. H. El-Sagheer, M. Lecerf, D. Patin, D. Mellal, C. Mayer, D. Blanot, N. Gale, T. Brown, H. Van Tilbeurgh, M. Etheve-Quelquejeu, M. Arthur
The Structure Of Femxwv In Complex With A Peptidyl-Rna Conjugate: Mechanism Of Aminoacyl Transfer From Ala-Trna(Ala) To Peptidoglycan Precursors
Angew. Chem. Int. Ed. Engl. V. 52 7278 2013
PubMed-ID: 23744707  |  Reference-DOI: 10.1002/ANIE.201301411

(-) Compounds

Molecule 1 - FEMX
    ChainsA
    EC Number2.3.2.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC-HIS60
    Expression System StrainTOP10
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFEMX
    Organism ScientificWEISSELLA VIRIDESCENS
    Organism Taxid1629
    StrainCIP102810T
 
Molecule 2 - 5-MER PEPTIDE
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES
 
Molecule 3 - RNA (5'-R(P*CP*CP*(A9Z))-3')
    ChainsC
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric/Biological Unit (6, 7)
No.NameCountTypeFull Name
1A9Z1Mod. Nucleotide2'-DEOXY-2'-(4-ETHYL-1H-1,2,3-TRIAZOL-1-YL)ADENOSINE5'-(DIHYDROGEN PHOSPHATE)
2DAL2Mod. Amino AcidD-ALANINE
3FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
4GOL1Ligand/IonGLYCEROL
5MUB1Ligand/IonN-ACETYLMURAMIC ACID
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:142 , GLN A:143 , ARG A:211 , TYR A:256 , CYS B:5 , DAL B:7 , HOH B:201 , HOH B:202BINDING SITE FOR RESIDUE DAL B 6
2AC2SOFTWARETRP A:32 , LYS A:36 , GLN A:143 , ARG A:211 , TYR A:215 , TYR A:256 , CYS B:5 , DAL B:6 , HOH B:203BINDING SITE FOR RESIDUE DAL B 7
3AC3SOFTWARELYS A:36 , ASN A:38 , TRP A:39 , THR A:64 , PHE A:70 , TYR A:103 , ARG A:106 , ILE A:142 , ARG A:211 , HOH A:509 , HOH A:552 , HOH A:619 , HOH A:663 , HOH A:752 , MUB B:102 , HOH B:203 , HOH B:208BINDING SITE FOR RESIDUE UDP B 101
4AC4SOFTWAREPHE A:17 , ILE A:54 , MET A:79 , ASP A:80 , LEU A:86 , ILE A:213 , GLU A:214 , HOH A:523 , HOH A:533 , HOH A:544BINDING SITE FOR RESIDUE GOL A 402
5AC5SOFTWARETHR A:209 , ARG A:211 , HOH A:535 , HOH A:722 , ALA B:3 , FGA B:4 , UDP B:101 , HOH B:201 , HOH B:202 , HOH B:205 , HOH B:206 , HOH B:208BINDING SITE FOR RESIDUE MUB B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4II9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:76 -Pro A:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4II9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4II9)

(-) Exons   (0, 0)

(no "Exon" information available for 4II9)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeeeee.....eeeeeeeeee......eeeee.........hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh..eee...hhhhhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeeeeeee..eeeeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh....ee...eeeee.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ii9 A   1 PVLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNNWEPVDVYLEDDQGAIIAAMSMLLGDTPTDKKFAYASKGPVMDVTDVDLLDRLVDEAVKALDGRAYVLRFDPEVAYSDEFNTTLQDHGYVTRNRNVADAGMHATIQPRLNMVLDLTKFPDAKTTLDLYPSKTKSKIKRPFRDGVEVHSGNSATELDEFFKTYTTMAERHGITHRPIEYFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALDTNTDLYDLGGIESESTDDSLYVFKHVFVKDAPREYIGEIDKVLDPEVYAELVKDGH 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ii9 B   3 AxCxx   7
                             | ||
                             4-FGA
                               6-DAL
                                7-DAL

Chain C from PDB  Type:DNA/RNA  Length:3
                                   
                 4ii9 C   8 CCa  10
                              |
                              |
                             10-A9Z

   Legend:   → Mismatch (orange background)
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  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 4II9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4II9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4II9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:76 - Pro A:77   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        FEMX_WEIVI | Q9EY501ne9 1p4n 1xe4 1xf8 1xix 3gkr

(-) Related Entries Specified in the PDB File

1ne9 APO-FORM STRUCTURE
1p4n PROTEIN-SUBSTRATE COMPLEX
1xe4 K36M MUTANT
1xf8 Y254 MUTANT
1xix APO FORM STRUCTURE FORM II
3gkr PROTEIN-SUBSTRATE PRODUCT COMPLEX