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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE--D-ALANINE LIGASE FROM BACILLUS ANTHRACIS
 
Authors :  Y. Kim, R. Mulligan, J. Hasseman, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  12 Mar 11  (Deposition) - 30 Mar 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Structure, Ligase, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, R. Mulligan, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of D-Alanine--D-Alanine Ligase From Bacillus Anthracis
To Be Published
PubMed: search

(-) 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: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BAS2435, BA_2610, DDL, DDLB, GBAA_2610
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Strain: AMES
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 32)

Asymmetric/Biological Unit (2, 32)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , LYS A:136 , MSE A:259 , GLU A:260 , HOH A:401BINDING SITE FOR RESIDUE EDO A 311
2AC2SOFTWARELYS A:32 , TYR A:33 , ASP A:289 , GLU A:293BINDING SITE FOR RESIDUE EDO A 312
3AC3SOFTWARECYS B:92 , LYS B:95 , SER B:98 , LYS B:99 , MSE B:259 , VAL B:261BINDING SITE FOR RESIDUE EDO B 311
4AC4SOFTWARETYR A:204 , GLU B:260BINDING SITE FOR RESIDUE EDO B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R23)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:131 -Pro A:132
2Phe B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R23)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_BACAN61-72
 		  2A:61-72
B:61-72
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_BACAN239-266
 		  2A:239-266
B:239-266

(-) Exons   (0, 0)

(no "Exon" information available for 3R23)

(-) 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:304
 aligned with DDL_BACAN | Q81Q29 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:304
                             1                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    
            DDL_BACAN     - -MRIGVIMGGVSSEKQVSIMTGNEMIANLDKNKYEIVPITLNEKMDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNMLSSGICMDKNISKKILRYEGIETPDWIELTKMEDLNFDELDKLGFPLVVKPNSGGSSVGVKIVYDKDELISMLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHAAEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVDMMVKDGIPYVMEVNTLPGMTQASLLPKSADAAGIHYSKLLDMIIETSLRVRKEEG 303
               SCOP domains d3r23a2 A:0-93 D-Ala-D-Ala ligase, N-domain                                                   d3r23a1 A:94-303 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhh....eeee...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeee................eeeee.........eee.hhhhhhhhhhhhhh...eeeeee....eeeeeeee..ee...eeeee..eee....eee...eeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------DALA_DALA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r23 A   0 AmRIGVImGGVSSEKQVSImTGNEmIANLDKNKYEIVPITLNEKmDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNmLSSGICmDKNISKKILRYEGIETPDWIELTKmEDLNFDELDKLGFPLVVKPNSGGSSVGVKIVYDKDELISmLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHAAEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVDmmVKDGIPYVmEVNTLPGmTQASLLPKSADAAGIHYSKLLDmIIETSLRVRKEEG 303
                             |     | 9        19    |   29        39    |   49        59        69        79      | 89   |    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249|      259       269       279       289|      299    
                             |     7-MSE      19-MSE|                  44-MSE                                    86-MSE 93-MSE                  118-MSE                                 158-MSE                                                                                    249-MSE   259-MSE 267-MSE                290-MSE         
                             1-MSE                 24-MSE                                                                                                                                                                                                                           250-MSE                                                 


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with DDL_BACAN | Q81Q29 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:304
                             1                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299    
            DDL_BACAN     - -MRIGVIMGGVSSEKQVSIMTGNEMIANLDKNKYEIVPITLNEKMDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNMLSSGICMDKNISKKILRYEGIETPDWIELTKMEDLNFDELDKLGFPLVVKPNSGGSSVGVKIVYDKDELISMLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHAAEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVDMMVKDGIPYVMEVNTLPGMTQASLLPKSADAAGIHYSKLLDMIIETSLRVRKEEG 303
               SCOP domains d3r23b2 B:0-93 D-Ala-D-Ala ligase, N-domain                                                   d3r23b1 B:94-303 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------Dala_Dala_lig_N-3r23B03 B:41-84             ----------------Dala_Dala_lig_C-3r23B01 B:101-293                                                                                                                                                                ---------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------Dala_Dala_lig_N-3r23B04 B:41-84             ----------------Dala_Dala_lig_C-3r23B02 B:101-293                                                                                                                                                                ---------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------Dala_Dala_lig_N-3r23B05 B:41-84             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------Dala_Dala_lig_N-3r23B06 B:41-84             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhh.....eeeee...----..eee...hhhhhhhhhhhhhh.eeeeee....eeeeeeee..ee...eeeee..eee....eee...eeee....hhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------DALA_DALA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r23 B   0 AmRIGVImGGVSSEKQVSImTGNEmIANLDKNKYEIVPITLNEKmDLIEKAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNmLSSGICmDKNISKKILRYEGIETPDWIELTKmEDLNFDELDKLGFPLVVKPNSG----GVKIVYDKDELISmLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHAAEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVDmmVKDGIPYVmEVNTLPGmTQASLLPKSADAAGIHYSKLLDmIIETSLRVRKEEG 303
                             |     | 9        19    |   29        39    |   49        59        69        79      | 89   |    99       109       119       129       139|    | 149       159       169       179       189       199       209       219       229       239       249|      259       269       279       289|      299    
                             1-MSE 7-MSE      19-MSE|                  44-MSE                                    86-MSE 93-MSE                  118-MSE               140  145          158-MSE                                                                                    249-MSE   259-MSE 267-MSE                290-MSE         
                                                   24-MSE                                                                                                                                                                                                                           250-MSE
   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 3R23)

(-) Pfam Domains  (2, 6)

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_BACAN | Q81Q29)
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

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UniProtKB/Swiss-Prot
        DDL_BACAN | Q81Q29: 3r5x

(-) Related Entries Specified in the PDB File

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