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(-) Description

Title :  CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMX:UDP-MURNAC-HEXAPEPTIDE COMPLEX
 
Authors :  V. Delfosse, J. Piton, R. Villet, M. Lecerf, M. Arthur, C. Mayer
Date :  11 Mar 09  (Deposition) - 23 Mar 10  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Femx, Peptidoglycan, Hexapeptide, Transferase, Transferase- Transferase Product Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Delfosse, J. Piton, R. Villet, M. Lecerf, M. Arthur, C. Mayer
Structure Of Weissella Viridescens Femx With The Udp-Murnac-Hexapeptide Product Of The Alanine Transfer Reaction
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FEMX
    Chains: A
    EC Number: 2.3.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FEMX
    Organism Scientific: LACTOBACILLUS VIRIDESCENS
    Organism Taxid: 1629
 
Molecule 2 - UDP-MURNAC-PEPTIDE
    Chains: B
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2DAL2Mod. Amino AcidD-ALANINE
3FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
4GOL1Ligand/IonGLYCEROL
5MG3Ligand/IonMAGNESIUM ION
6UMA1Mod. Amino AcidURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:64 , THR A:66 , HOH A:554 , HOH A:607 , HOH A:803BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWARELEU A:280 , ASN A:283 , HOH A:587 , HOH A:665 , HOH A:781 , HOH A:850BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARELEU A:150 , PHE A:308 , VAL A:309 , LYS A:310 , HOH A:662 , HOH A:829BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREILE A:54 , MET A:79 , ASP A:80 , LEU A:86 , ILE A:213 , GLU A:214 , HOH A:509 , HOH A:533 , HOH A:563BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREUMA B:1 , LYS B:3 , HOH B:214BINDING SITE FOR RESIDUE ALA B 101
6AC6SOFTWARETRP A:32 , LYS A:36 , ASN A:38 , TRP A:39 , PHE A:70 , ASP A:85 , TYR A:103 , ARG A:106 , ILE A:142 , ILE A:208 , THR A:209 , ARG A:211 , PRO A:212 , TYR A:215 , TYR A:256 , HOH A:535 , HOH A:667 , ALA B:101 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:206 , HOH B:207 , HOH B:208 , HOH B:209 , HOH B:210 , HOH B:211 , HOH B:212 , HOH B:213 , HOH B:215 , HOH B:216 , HOH B:217 , HOH B:218 , HOH B:220 , HOH B:221 , HOH B:222 , HOH B:223BINDING SITE FOR CHAIN B OF UDP-MURNAC- PENTAPEPTIDE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GKR)

(-) 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 3GKR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GKR)

(-) Exons   (0, 0)

(no "Exon" information available for 3GKR)

(-) 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:335
 aligned with FEMX_WEIVI | Q9EY50 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:335
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331     
           FEMX_WEIVI     2 PVLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNNWEPVDVYLEDDQGAIIAAMSMLLGDTPTDKKFAYASKGPVMDVTDVDLLDRLVDEAVKALDGRAYVLRFDPEVAYSDEFNTTLQDHGYVTRNRNVADAGMHATIQPRLNMVLDLTKFPDAKTTLDLYPSKTKSKIKRPFRDGVEVHSGNSATELDEFFKTYTTMAERHGITHRPIEYFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALDTNTDLYDLGGIESESTDDSLYVFKHVFVKDAPREYIGEIDKVLDPEVYAELVKD 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gkrA01 A:1-143,A:315-335  [code=3.40.630.30, no name defined]                                                                                 ----3gkrA02 A:148-312  [code=3.40.630.30, no name defined]                                                                                                               --3gkrA01               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeeeee.....eeeeeeeeee......eeeee.........hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh..eeehhhhh...........eeeeee.hhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeeeeeee..eeeeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh....ee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gkr A   1 PVLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNNWEPVDVYLEDDQGAIIAAMSMLLGDTPTDKKFAYASKGPVMDVTDVDLLDRLVDEAVKALDGRAYVLRFDPEVAYSDEFNTTLQDHGYVTRNRNVADAGMHATIQPRLNMVLDLTKFPDAKTTLDLYPSKTKSKIKRPFRDGVEVHSGNSATELDEFFKTYTTMAERHGITHRPIEYFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALDTNTDLYDLGGIESESTDDSLYVFKHVFVKDAPREYIGEIDKVLDPEVYAELVKD 335
                                    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
                 3gkr B   1 axKxx   5
                            || ||
                            1-UMA
                             2-FGA
                               4-DAL
                                5-DAL
   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 3GKR)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GKR)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FEMX_WEIVI | Q9EY50)
molecular function
    GO:0047206    UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity    Catalysis of the reaction: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine + L-alanyl-tRNA = UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-N6-(L-alanyl)-L-lysyl-D-alanyl-D-alanine + tRNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016755    transferase activity, transferring amino-acyl groups    Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FEMX_WEIVI | Q9EY50: 1ne9 1p4n 1xe4 1xf8 1xix 4ii9

(-) 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