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(-) Description

Title :  COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE
 
Authors :  J. R. Knox, P. C. Moews, C. Fan
Date :  20 Sep 96  (Deposition) - 12 Feb 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycogen Phosphorylase, Ligase, Cell Wall, Peptidoglycan Synthesis, Vancomycin, Adp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Fan, I. S. Park, C. T. Walsh, J. R. Knox
D-Alanine:D-Alanine Ligase: Phosphonate And Phosphinate Intermediates With Wild Type And The Y216F Mutant.
Biochemistry V. 36 2531 1997
PubMed-ID: 9054558  |  Reference-DOI: 10.1021/BI962431T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALA:D-ALA LIGASE
    ChainsA
    EC Number6.3.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneDDLB
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsENZYME PROVIDED BY C.T. WALSH, HARVARD MED SCHOOL. SEE ZAWADZKE ET AL. BIOCHEM. 30, P. 1673, 1991.

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3POB1Ligand/Ion2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHINOYLOXY]-BUTYRICACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:257 , GLU A:270 , ADP A:310 , POB A:321BINDING SITE FOR RESIDUE MG A 330
2AC2SOFTWAREGLY A:149 , GLU A:270 , ASN A:272 , ADP A:310 , POB A:321 , HOH A:536BINDING SITE FOR RESIDUE MG A 331
3AC3SOFTWARESER A:94 , GLU A:270 , ALA A:271 , HOH A:522BINDING SITE FOR RESIDUE MG A 332
4AC4SOFTWARELYS A:97 , ILE A:142 , LYS A:144 , GLU A:148 , GLY A:149 , SER A:150 , SER A:151 , MET A:154 , GLU A:180 , LYS A:181 , TRP A:182 , LEU A:183 , GLU A:187 , TYR A:210 , LYS A:215 , ASP A:257 , MET A:259 , LEU A:269 , GLU A:270 , POB A:321 , MG A:330 , MG A:331 , HOH A:511BINDING SITE FOR RESIDUE ADP A 310
5AC5SOFTWAREGLU A:15 , GLY A:149 , SER A:150 , TYR A:210 , LYS A:215 , TYR A:216 , ARG A:255 , ASP A:257 , GLU A:270 , ASN A:272 , PRO A:275 , GLY A:276 , SER A:281 , LEU A:282 , ADP A:310 , MG A:330 , MG A:331 , HOH A:508 , HOH A:536 , HOH A:538BINDING SITE FOR RESIDUE POB A 321
6ADPUNKNOWNLYS A:97 , LYS A:144 , LYS A:215 , GLU A:270 , ASN A:272 , SER A:151 , GLU A:180 , GLU A:187 , TRP A:182 , ALA A:159 , ILE A:142 , PHE A:209ADP BINDING SITE.
7LIGUNKNOWNGLU A:15 , SER A:150 , TYR A:216 , VAL A:18 , HIS A:63 , SER A:281LIGAND BINDING SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IOV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:139 -Pro A:140
2Cys A:225 -Pro A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IOV)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDLB_ECOLI63-74  1A:63-74
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDLB_ECOLI248-276  1A:248-276

(-) Exons   (0, 0)

(no "Exon" information available for 1IOV)

(-) 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:306
 aligned with DDLB_ECOLI | P07862 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:306
                                    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      
           DDLB_ECOLI     1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
               SCOP domains d1iova1 A:1-96 D-Ala-D-Ala ligase, N-domain                                                     d1iova2 A:97-306 D-ala-D-ala ligase, C-domain                                                                                                                                                                      SCOP domains
               CATH domains 1iovA01 A:1-84  [code=3.40.50.20, no name defined]                                  1iovA02 A:85-110,A:184-3061iovA03 A:111-183 ATP-grasp fold, A domain                               1iovA02 A:85-110,A:184-306 ATP-grasp fold, B domain                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh...eeeeee.............eeeeeee.........hhhhhhhhh........hhhhhhh..hhhhhhhhhh.......eeeeehhhh........hhhhhh....eeeee.........eee..hhhhhhhhhhhhh...eeeeee.....eeeeeee.......eeee.......hhhhh.....eee........hhhhhhhhhhhhhh......eeeeeeee.....eeeeeee.........hhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iov A   1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
                                    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      

   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IOV)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DDLB_ECOLI | P07862)
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        DDLB_ECOLI | P078621iow 2dln 4c5a 4c5b 4c5c

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