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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP-MURNAC-ALA-GLU-LYS AND ADP
 
Authors :  V. Fulop, D. I. Roper, K. M. Ruane, H. Barreteau, A. Boniface, S. Dementi D. Blanot, D. Mengin-Lecreulx, S. Gobec, A. Dessen, C. G. Dowson, A. J.
Date :  09 Aug 13  (Deposition) - 02 Oct 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Ruane, A. J. Lloyd, V. Fulop, C. G. Dowson, H. Barreteau, A. Boniface, S. Dementin, D. Blanot, D. Mengin-Lecreulx, S. Gobec, A. Dessen, D. I. Roper
Specificity Determinants For Lysine Incorporation In Staphylococcus Aureus Peptidoglycan As Revealed By The Structure Of A Mure Enzyme Ternary Complex.
J. Biol. Chem. V. 288 33439 2013
PubMed-ID: 24064214  |  Reference-DOI: 10.1074/JBC.M113.508135

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE
    Chains: A
    EC Number: 6.3.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET2160
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: K219 HAS BEEN MODIFIED BY CARBAMOYLATION
    Strain: 8325
    Synonym: L-LYSINE-ADDING ENZYME, UDP-MURNAC-L-ALA-D-GLU:L-LYS LIGASE, UDP-MURNAC-TRIPEPTIDE SYNTHETASE, UDP-N-ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MG2Ligand/IonMAGNESIUM ION
5UML1Ligand/IonURIDINE 5'DIPHOSPHO N-ACETYL MURAMOYL-L-ALANYL-D-GLUTAMYL-L-LYSINE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5UML2Ligand/IonURIDINE 5'DIPHOSPHO N-ACETYL MURAMOYL-L-ALANYL-D-GLUTAMYL-L-LYSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:28 , ASP A:29 , SER A:30 , ARG A:31 , GLY A:44 , TYR A:45 , THR A:46 , VAL A:47 , SER A:49 , PHE A:52 , ASN A:151 , THR A:152 , THR A:153 , GLU A:155 , SER A:179 , HIS A:181 , ARG A:187 , HIS A:205 , TYR A:351 , ARG A:383 , ASP A:406 , SER A:456 , GLU A:460 , HOH A:2045 , HOH A:2049 , HOH A:2058 , HOH A:2206 , HOH A:2208 , HOH A:2396 , HOH A:2422 , HOH A:2479 , HOH A:2480 , HOH A:2481 , HOH A:2482 , HOH A:2483 , HOH A:2484 , HOH A:2485 , HOH A:2486 , HOH A:2487BINDING SITE FOR RESIDUE UML A1498
2AC2SOFTWARETHR A:111 , ASN A:112 , GLY A:113 , LYS A:114 , THR A:115 , SER A:116 , GLU A:177 , ASN A:200 , PHE A:300 , ASN A:304 , ARG A:335 , ASP A:350 , TYR A:351 , ALA A:352 , HIS A:353 , ASP A:356 , GLY A:357 , LYS A:360 , MG A:1500 , HOH A:2143 , HOH A:2144 , HOH A:2152 , HOH A:2241 , HOH A:2488BINDING SITE FOR RESIDUE ADP A1499
3AC3SOFTWARETHR A:115 , THR A:137 , GLU A:177 , ADP A:1499 , HOH A:2152 , HOH A:2181BINDING SITE FOR RESIDUE MG A1500
4AC4SOFTWARETHR A:111 , LYS A:114 , HIS A:205 , KCX A:219 , HOH A:2151BINDING SITE FOR RESIDUE MG A1501
5AC5SOFTWAREMET A:212 , GLU A:213 , GOL A:1495 , HOH A:2489BINDING SITE FOR RESIDUE GOL A1494
6AC6SOFTWAREGLU A:213 , HIS A:217 , PHE A:244 , TYR A:247 , GOL A:1494 , HOH A:2261BINDING SITE FOR RESIDUE GOL A1495

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C12)

(-) Exons   (0, 0)

(no "Exon" information available for 4C12)

(-) Sequences/Alignments

Asymmetric 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:493
 aligned with MURE_STAA8 | Q2FZP6 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:493
                                    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       440       450       460       470       480       490   
           MURE_STAA8     1 MDASTLFKKVKVKRVLGSLEQQIDDITTDSRTAREGSIFVASVGYTVDSHKFCQNVADQGCKLVVVNKEQSLPANVTQVVVPDTLRVASILAHTLYDYPSHQLVTFGVTGTNGKTSIATMIHLIQRKLQKNSAYLGTNGFQINETKTKGANTTPETVSLTKKIKEAVDAGAESMTLEVSSHGLVLGRLRGVEFDVAIFSNLTQDHLDFHGTMEAYGHAKSLLFSQLGEDLSKEKYVVLNNDDSFSEYLRTVTPYEVFSYGIDEEAQFMAKNIQESLQGVSFDFVTPFGTYPVKSPYVGKFNISNIMAAMIAVWSKGTSLETIIKAVENLEPVEGRLEVLDPSLPIDLIIDYAHTADGMNKLIDAVQPFVKQKLIFLVGMAGERDLTKTPEMGRVACRADYVIFTPDNPANDDPKMLTAELAKGATHQNYIEFDDRAEGIKHAIDIAEPGDTVVLASKGREPYQIMPGHIKVPHRDDLIGLEAAYKKFGGGPVD 493
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....eee........eee.hhhhh...eeee........hhhhhhhhhhh...eeee..........eeee..hhhhhhhhhhhhhh.hhhhh.eeeeee...hhhhhhhhhhhhhhhh...eeeee..eeee..eee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.........eeee......hhhhhhhhhhhhhhhhhhhhh.........eeeee....hhhhhhh....eeeeee......eeeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........ee.......eeeee...hhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhh...eeeeeee.....hhhhhhhhhhh......eee..hhhhhhhhhhhhh....eeeee......eeeehhheeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c12 A   1 MDASTLFKKVKVKRVLGSLEQQIDDITTDSRTAREGSIFVASVGYTVDSHKFCQNVADQGCKLVVVNKEQSLPANVTQVVVPDTLRVASILAHTLYDYPSHQLVTFGVTGTNGKTSIATMIHLIQRKLQKNSAYLGTNGFQINETKTKGANTTPETVSLTKKIKEAVDAGAESMTLEVSSHGLVLGRLRGVEFDVAIFSNLTQDHLDFHGTMEAYGHAkSLLFSQLGEDLSKEKYVVLNNDDSFSEYLRTVTPYEVFSYGIDEEAQFMAKNIQESLQGVSFDFVTPFGTYPVKSPYVGKFNISNIMAAMIAVWSKGTSLETIIKAVENLEPVEGRLEVLDPSLPIDLIIDYAHTADGMNKLIDAVQPFVKQKLIFLVGMAGERDLTKTPEMGRVACRADYVIFTPDNPANDDPKMLTAELAKGATHQNYIEFDDRAEGIKHAIDIAEPGDTVVLASKGREPYQIMPGHIKVPHRDDLIGLEAAYKKFGGGPVD 493
                                    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       440       450       460       470       480       490   
                                                                                                                                                                                                                                                    219-KCX
   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 4C12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C12)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (MURE_STAA8 | Q2FZP6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047482    UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity    Catalysis of the reaction: L-lysine + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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

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        MURE_STAA8 | Q2FZP6: 4c13

(-) Related Entries Specified in the PDB File

4c13 X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP-MURNAC-ALA-GLU-LYS