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(-) Description

Title :  CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
 
Authors :  M. Kotnik, J. Humljan, C. Contreras-Martel, M. Oblak, K. Kristan, M. Herve, D. Blanot, U. Urleb, S. Gobec, A. Dessen, T. Solmajer
Date :  01 Feb 07  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Murd-Inhibitor Complex, Peptidoglycan Synthesis, Ligase, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Sulfonamide Inhibitor, Murd Ligase, Atp-Binding, Cell Division (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kotnik, J. Humljan, C. Contreras-Martel, M. Oblak, K. Kristan, M. Herve, D. Blanot, U. Urleb, S. Gobec, A. Dessen, T. Solmajer
Structural And Functional Characterization Of Enantiomeric Glutamic Acid Derivatives As Potential Transition State Analogue Inhibitors Of Murd Ligase.
J. Mol. Biol. V. 370 107 2007
PubMed-ID: 17507028  |  Reference-DOI: 10.1016/J.JMB.2007.04.048

(-) 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 Cell Line: DH5A
    Expression System Plasmid: PABD16
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: INHIBITOR N-(6-BUTOXY-NAPHTHALENE-2- SULFONYL)-D-GLUTAMIC ACID BOUND
    Synonym: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE LIGASE, UDP-N- ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D-GLUTAMIC ACID- ADDING ENZYME

 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
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2LK21Ligand/IonN-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC ACID
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , LYS A:319 , HOH A:2478 , HOH A:2479BINDING SITE FOR RESIDUE SO4 A1441
2AC2SOFTWAREHIS A:309 , ASN A:310 , SER A:438 , HIS A:439BINDING SITE FOR RESIDUE SO4 A1442
3AC3SOFTWAREASP A:35 , ARG A:37 , SER A:71 , GLY A:73 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , HOH A:2191 , HOH A:2218 , HOH A:2247 , HOH A:2474 , HOH A:2475 , HOH A:2476 , HOH A:2477BINDING SITE FOR RESIDUE LK2 A1440

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:208 -A:227
2A:208 -A:227

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JFF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JFF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JFF)

(-) Exons   (0, 0)

(no "Exon" information available for 2JFF)

(-) 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:433
 aligned with MURD_ECOLI | P14900 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              438  
                                    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       341       351       361       371       381       391       401       411       421       431      |  
           MURD_ECOLI     2 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG--   -
               SCOP domains d2jffa1 A:1-93 automated matches                                                             d2jffa3 A:94-297 automated matches                                                                                                                                                                          d2jffa2 A:298-439 automated matches                                                                                                            SCOP domains
               CATH domains 2jffA01 A:1-92 NAD(P)-binding Rossmann-like Domain                                          2jffA02 A:93-298  [code=3.40.1190.10, no name defined]                                                                                                                                                        2jffA03 A:299-433  [code=3.90.190.20, no name defined]                                                                                 ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------Mur_ligase_M-2jffA02 A:109-279                                                                                                                                             -------------------Mur_ligase_C-2jffA01 A:299-378                                                  ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.hhhhhhhhhhhhhh.....eeee......hhhhh.....eee...hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee......hhhhh.hhhhhhhhhhhhhhh...eeeee..hhhhh...----..eee......eeeee.--.eeeee..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
                 2jff A   1 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAkLRIYENAKVCVVNADDALTMPIR----RCVSFGVNMGDYHLNHQ--ETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH 439
                                    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       340       350       360       370       380       390       400       410       420       430         
                                                                                                                                                                                                                               198-KCX                221  226             242  |                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                              245
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Mur_ligase_C] (24)
(-)
Clan: no clan defined [family: Mur_ligase_M] (23)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MURD_ECOLI | P14900)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008764    UDP-N-acetylmuramoylalanine-D-glutamate ligase activity    Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MURD_ECOLI | P14900: 1e0d 1eeh 1uag 2jfg 2jfh 2uag 2uuo 2uup 2vtd 2vte 2wjp 2x5o 2xpc 2y1o 2y66 2y67 2y68 3uag 4uag 5a5e 5a5f

(-) Related Entries Specified in the PDB File

1e0d UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
1eeh UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
1uag UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
2jfg CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP
2jfh CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH L-GLU CONTAINING SULFONAMIDE INHIBITOR
2uag UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
3uag UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
4uag UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE