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(-) Description

Title :  ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D-ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES
 
Authors :  S. Liu, J. S. Chang, J. T. Herberg, M. Horng, P. K. Tomich, A. H. Lin, K. R. M
Date :  01 Sep 06  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  D-Alanine:D-Alanine Ligase, Apo, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Liu, J. S. Chang, J. T. Herberg, M. M. Horng, P. K. Tomich, A. H. Lin, K. R. Marotti
Allosteric Inhibition Of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies.
Proc. Natl. Acad. Sci. Usa V. 103 15178 2006
PubMed-ID: 17015835  |  Reference-DOI: 10.1073/PNAS.0604905103

(-) Compounds

Molecule 1 - D-ALANINE-D-ALANINE LIGASE
    ChainsA, B
    EC Number6.3.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-60
    Expression System StrainM15[PREP4]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDDL
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid93062
    StrainCOL
    SynonymD-ALANYLALANINE SYNTHETASE, D-ALA-D-ALA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:291 , ASN A:308 , PRO A:311 , GLY A:312BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREARG B:291 , ASN B:308 , PRO B:311 , GLY B:312BINDING SITE FOR RESIDUE SO4 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I87)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:172 -Pro A:173
2Ile A:261 -Pro A:262
3Tyr B:172 -Pro B:173
4Ile B:261 -Pro B:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I87)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_STAAC96-107
 
  2A:96-107
B:96-107
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_STAAC284-312
 
  2A:284-312
B:284-312

(-) Exons   (0, 0)

(no "Exon" information available for 2I87)

(-) 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:345
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:356
                                                                                                                                                                                                                                                                                                                                                                                           356  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   |  
            DDL_STAAC     3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID--   -
               SCOP domains d2i87a1 A:3-128 automated matches                                                                                             d2i87a2 A:129-358 automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhh.....eeeeeeee.....eeee........hhhhhhhhhheee..hhhhhh........eeeee........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhhh...eeeeee....eeeeeeeee....ee...eee......-----------..ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i87 A   3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAF-----------VQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDRS 358
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |      -    |  262       272       282       292       302       312       322       332       342       352      
                                                                                                                                                                                                                                                                            245         257                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:358
                                                                                                                                                                                                                                                                                                                                                                                           356    
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   |    
            DDL_STAAC     3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID----   -
               SCOP domains d2i87b1 B:3-128 automated matches                                                                                             d2i87b2 B:129-360 automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee........hhhhhh.....-.hhhhhhhh........eeee.....--..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee....ee...eee......-----------..ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i87 B   3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGE-LEISQLLKESSSGQPYDAVFPLLHGP--EDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAF-----------VQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDRSHH 360
                                    12        22        32        42        52        62        |-|       82        92     | 102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |      -    |  262       272       282       292       302       312       322       332       342       352        
                                                                                               71 |                       98  |                                                                                                                                             245         257                                                                                                       
                                                                                                 73                         101                                                                                                                                                                                                                                                                   

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I87)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDL_STAAC | Q5HEB7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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
        DDL_STAAC | Q5HEB72i80 2i8c 3n8d

(-) Related Entries Specified in the PDB File

2i80 ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D- ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES
2i8c ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D- ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES