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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORM OF D-ALANINE:D-ALANINE LIGASE (DDL) FROM STREPTOCOCCUS MUTANS
 
Authors :  Y. Lu
Date :  03 Oct 09  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  D-Alanyl-Alanine Synthetase, Atp-Binding, Cell Shape, Cell Wall Biogenesis/Degradation, Ligase, Magnesium, Manganese, Metal-Binding, Nucleotide-Binding, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Lu, H. Xu, X. Zhao
Crystal Structure Of The Apo Form Of D-Alanine:D-Alanine Ligase (Ddl) From Streptococcus Mutans
Protein Pept. Lett. V. 17 1053 2010
PubMed-ID: 20522004

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDL
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 1309
    Strain: UA159
    Synonym: D-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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3K3P)

(-) Sites  (0, 0)

(no "Site" information available for 3K3P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K3P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:168 -Pro A:169
2Ile A:257 -Pro A:258
3Tyr B:168 -Pro B:169
4Ile B:257 -Pro B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K3P)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_STRMU94-105
 		  2A:94-105
B:94-105
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_STRMU280-308
 		  2A:280-308
B:280-308

(-) Exons   (0, 0)

(no "Exon" information available for 3K3P)

(-) 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:317
 aligned with DDL_STRMU | P95803 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:344
                                    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    
            DDL_STRMU     3 KETLVLLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQAGDFIKTQEFDSQPSETDKLMTNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQVAYVALIEGEPLESKLAEVEEKLIYPVFVKPANMGSSVGISKAENRTDLKQAIALALKYDSRVLIEQGVDAREIEVGILGNTDVKTTLPGEIVKDVAFYDYEAKYIDNKITMAIPAEIDPVIVEKMRDYAATAFRTLGCCGLSRCDFFLTEDGKVYLNELNTMPGFTQWSMYPLLWENMGLSYSVLIEELVSLAKEMFDKRES 346
               SCOP domains d3k3pa1 A:3-126 automated matches                                                                                           d3k3pa2 A:127-346 automated matches                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee.....--.........hhh.eehhhhhh....eeeee........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh...eeeee..------.eee.hhhhhhhhhhhhhhhh.eeeeee....eeeeeeeee....ee...eee.-----------------........hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee......--hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3p A   3 KETLVLLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQAGDFIKTQEFDSQPS--DKLMTNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQVAYVALIEGEPLESKLAEVEEKLIYPVFVKPAN------ISKAENRTDLKQAIALALKYDSRVLIEQGVDAREIEVGILGNTDVKTTLPGEIV-----------------TMAIPAEIDPVIVEKMRDYAATAFRTLGCCGLSRCDFFLTEDGKVYLNELNTMPGFT--SMYPLLWENMGLSYSVLIEELVSLAKEMFDKRES 346
                                    12        22        32        42        52       | -|       72        82        92       102       112       122       132       142       152       162       172   |     -|      192       202       212       222       232   |     -         - |     262       272       282       292       302       | -|      322       332       342    
                                                                                    60 63                                                                                                              176    183                                                  236               254                                                     310  |                                 
                                                                                                                                                                                                                                                                                                                                                313                                 


Chain B from PDB  Type:PROTEIN  Length:318
 aligned with DDL_STRMU | P95803 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:344
                                    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    
            DDL_STRMU     3 KETLVLLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQAGDFIKTQEFDSQPSETDKLMTNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQVAYVALIEGEPLESKLAEVEEKLIYPVFVKPANMGSSVGISKAENRTDLKQAIALALKYDSRVLIEQGVDAREIEVGILGNTDVKTTLPGEIVKDVAFYDYEAKYIDNKITMAIPAEIDPVIVEKMRDYAATAFRTLGCCGLSRCDFFLTEDGKVYLNELNTMPGFTQWSMYPLLWENMGLSYSVLIEELVSLAKEMFDKRES 346
               SCOP domains d3k3pb1 B:3-126 automated matches                                                                                           d3k3pb2 B:127-346 automated matches                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Dala_Dala_lig_N-3k3pB03 B:4-117                                                                                   --Dala_Dala_lig_C-3k3pB01 B:120-335                                                                                                                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -Dala_Dala_lig_N-3k3pB04 B:4-117                                                                                   --Dala_Dala_lig_C-3k3pB02 B:120-335                                                                                                                                                                                       ----------- Pfam domains (2)
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee.....--.........hhh.eehhhhhh....eeeee........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh...eeeee..-----..eee.hhhhhhhhhhhhhhhh.eeeeee....eeeeeeeee....ee...eee.-----------------........hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeee......--hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------DALA_DALA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3p B   3 KETLVLLYGGRSAERDVSVLSAESVMRAINYDNFLVKTYFITQAGDFIKTQEFDSQPS--DKLMTNDTIIASQKIKPSDIYEEEAVVFPVLHGPMGEDGSIQGFLEVLKMPYVGTNILSSSVAMDKITTNQVLESATTIPQVAYVALIEGEPLESKLAEVEEKLIYPVFVKPAN-----GISKAENRTDLKQAIALALKYDSRVLIEQGVDAREIEVGILGNTDVKTTLPGEIV-----------------TMAIPAEIDPVIVEKMRDYAATAFRTLGCCGLSRCDFFLTEDGKVYLNELNTMPGFT--SMYPLLWENMGLSYSVLIEELVSLAKEMFDKRES 346
                                    12        22        32        42        52       | -|       72        82        92       102       112       122       132       142       152       162       172   |   182       192       202       212       222       232   |     -         - |     262       272       282       292       302       | -|      322       332       342    
                                                                                    60 63                                                                                                              176   182                                                   236               254                                                     310  |                                 
                                                                                                                                                                                                                                                                                                                                                313
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K3P)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)
(-)
Clan: no clan defined [family: Dala_Dala_lig_N] (12)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDL_STRMU | P95803)
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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    Ile A:257 - Pro A:258   [ RasMol ]  
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    Tyr A:168 - Pro A:169   [ RasMol ]  
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