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(-) Description

Title :  CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP
 
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 :  1.90
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, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MLI2Ligand/IonMALONATE ION
3UMA1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , LEU A:15 , THR A:16 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , PRO A:72 , GLY A:73 , GLY A:137 , ASN A:138 , GLY A:140 , SER A:159 , GLN A:162 , HIS A:183 , HOH A:2009 , HOH A:2010 , HOH A:2012 , HOH A:2059 , HOH A:2071 , HOH A:2095 , HOH A:2265 , HOH A:2266 , HOH A:2267BINDING SITE FOR RESIDUE UMA A 450
2AC2SOFTWAREASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ASN A:178 , HIS A:267 , ASN A:271 , ARG A:302 , PHE A:303 , ASP A:317 , LYS A:319 , ALA A:320 , SER A:325 , ALA A:328 , HOH A:2068 , HOH A:2071 , HOH A:2072 , HOH A:2074 , HOH A:2119 , HOH A:2184 , HOH A:2268BINDING SITE FOR RESIDUE ADP A 451
3AC3SOFTWARETHR A:321 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , HOH A:2212BINDING SITE FOR RESIDUE MLI A 500
4AC4SOFTWAREHIS A:241 , THR A:246 , HIS A:334 , HOH A:2181 , HOH A:2269BINDING SITE FOR RESIDUE MLI A 501

(-) 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 5A5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A5F)

(-) Exons   (0, 0)

(no "Exon" information available for 5A5F)

(-) 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    
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Chain A from PDB  Type:PROTEIN  Length:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..hhhhhhhhhhhhhh....eeee......hhhhh.....eee...hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee......hhhhh..hhhhhhhhhhhhhh...eeeee..hhhhh....eee......eeeeee..eeeeee..eeeee.hhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeee..eeeee.....hhhhhhhhhhh......eeeeee.......hhhhhhhh....eeeeee..hhhhhhhhhhh.eee..hhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a5f A   1 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGS 438
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220||     235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435   
                                                                                                                                                                                                                                                      221|                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                       227
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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 5A5F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A5F)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a5f
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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 5a5e

(-) Related Entries Specified in the PDB File

5a5e CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI