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(-) Description

Title :  CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI
 
Authors :  R. Sink, M. Kotnik, A. Zega, H. Barreteau, S. Gobec, D. Blanot, A. Dessen C. Contreras-Martel
Date :  17 Jun 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Peptidoglycan Synthesis, Adp-Forming Enzyme, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Atp- Binding, Cell Division, Ligand, Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sink, M. Kotnik, A. Zega, H. Barreteau, S. Gobec, D. Blanot, A. Dessen, C. Contreras-Martel
Crystallographic Study Of Peptidoglycan Biosynthesis Enzyme Murd: Domain Movement Revisited.
Plos One V. 11 52075 2016
PubMed-ID: 27031227  |  Reference-DOI: 10.1371/JOURNAL.PONE.0152075

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
    Chains: A
    EC Number: 6.3.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 668369
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: D-GLUTAMIC ACID-ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L-ALANY L-D-GLUTAMATE SYNTHETASE, MURD LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NI1Ligand/IonNICKEL (II) ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:15 , ALA A:212 , MET A:218 , SER A:229 , HOH A:2020BINDING SITE FOR RESIDUE MPD A 502
2AC2SOFTWAREGLU A:253 , HIS A:309BINDING SITE FOR RESIDUE NI A 650
3AC3SOFTWAREGLY A:111 , LYS A:115 , SER A:160 , TYR A:194 , LYS A:198 , HOH A:2109 , HOH A:2124BINDING SITE FOR RESIDUE SO4 A 800
4AC4SOFTWARETHR A:321 , ALA A:414 , SER A:415 , LEU A:416 , ASN A:421 , PHE A:422 , HOH A:2297BINDING SITE FOR RESIDUE SO4 A 801
5AC5SOFTWARESER A:264 , GLY A:265 , TYR A:269 , HIS A:334 , HOH A:2192BINDING SITE FOR RESIDUE SO4 A 802
6AC6SOFTWAREALA A:282 , GLY A:283 , ARG A:400BINDING SITE FOR RESIDUE SO4 A 803
7AC7SOFTWAREGLY A:14 , LEU A:15 , THR A:16 , HOH A:2010 , HOH A:2011 , HOH A:2059BINDING SITE FOR RESIDUE SO4 A 804
8AC8SOFTWAREGLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , LYS A:319 , HOH A:2096 , HOH A:2234BINDING SITE FOR RESIDUE SO4 A1441

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:208 -A:227

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A5E)

(-) Exons   (0, 0)

(no "Exon" information available for 5A5E)

(-) 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:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..hhhhhhhhhhhhhh....eeee....hhhhhhh.....eee...hhhhhhhh.eeee..hhhhhhhhhhhhhhh..eeehhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee.......hhhhhhhhhhhhhh...eeeee..hhhhh........eeee......eeeeee..eeeeee..eeeee.hhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeee..eeeee.....hhhhhhhhhh.......eeeeee.......hhhhhhhh....eeeeee..hhhhhhhhhhh.eee..hhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a5e A   1 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436 
                                                                                                                                                                                                             180|                                                                                                                                                                                                                                                          
                                                                                                                                                                                                              187
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5A5E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A5E)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a5e
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  MURD_ECOLI | P14900
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  6.3.2.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        MURD_ECOLI | P14900: 1e0d 1eeh 1uag 2jff 2jfg 2jfh 2uag 2uuo 2uup 2vtd 2vte 2wjp 2x5o 2xpc 2y1o 2y66 2y67 2y68 3uag 4uag 5a5f

(-) Related Entries Specified in the PDB File

5a5f CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP