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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS CEREUS D-ALANYL CARRIER PROTEIN LIGASE DLTA IN COMPLEX WITH ATP: IMPLICATIONS FOR ADENYLATION MECHANISM
 
Authors :  K. T. Osman, L. Du, Y. He, Y. Luo
Date :  21 Nov 08  (Deposition) - 14 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Dlta, Amp-Forming Domain, D-Alanine, Adenylation, D-Alanine Carrier Protein Ligase, Atp Complex, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. T. Osman, L. Du, Y. He, Y. Luo
Crystal Structure Of Bacillus Cereus D-Alanyl Carrier Protein Ligase (Dlta) In Complex With Atp.
J. Mol. Biol. V. 388 345 2009
PubMed-ID: 19324056  |  Reference-DOI: 10.1016/J.JMB.2009.03.040

(-) Compounds

Molecule 1 - D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 1
    Chains: A
    EC Number: 6.1.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21-ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BC_1372, DLTA
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579
    Synonym: D-ALANINE-ACTIVATING ENZYME, DAE, D-ALANINE-D-ALANYL CARRIER PROTEIN LIGASE, DCL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREATP A:711 , HOH A:791 , HOH A:792 , HOH A:793 , HOH A:794BINDING SITE FOR RESIDUE CA A 710
2AC2SOFTWARETHR A:152 , SER A:153 , GLY A:154 , PHE A:196 , GLY A:270 , GLU A:271 , VAL A:272 , ASN A:292 , THR A:293 , TYR A:294 , GLY A:295 , THR A:297 , ASP A:383 , TYR A:394 , ARG A:397 , LYS A:492 , CA A:710 , HOH A:792 , HOH A:794 , HOH A:806 , HOH A:827 , HOH A:863 , HOH A:1157 , HOH A:1172BINDING SITE FOR RESIDUE ATP A 711

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FCE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.DLTA_BACCR149-160  1A:149-160

(-) Exons   (0, 0)

(no "Exon" information available for 3FCE)

(-) 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:500
 aligned with DLTA_BACCR | Q81G39 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:504
                                    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       500    
           DLTA_BACCR     1 MKLLEQIEKWAAETPDQTAFVWRDAKITYKQLKEDSDALAHWISSEYPDDRSPIMVYGHMQPEMIINFLGCVKAGHAYIPVDLSIPADRVQRIAENSGAKLLLSATAVTVTDLPVRIVSEDNLKDIFFTHKGNTPNPEHAVKGDENFYIIYTSGSTGNPKGVQITYNCLVSFTKWAVEDFNLQTGQVFLNQAPFSFDLSVMDIYPSLVTGGTLWAIDKDMIARPKDLFASLEQSDIQVWTSTPSFAEMCLMEASFSESMLPNMKTFLFCGEVLPNEVARKLIERFPKATIMNTYGPTEATVAVTGIHVTEEVLDQYKSLPVGYCKSDCRLLIMKEDGTIAPDGEKGEIVIVGPSVSVGYLGSPELTEKAFTMIDGERAYKTGDAGYVENGLLFYNGRLDFQIKLHGYRMELEEIEHHLRACSYVEGAVIVPIKKGEKYDYLLAVVVPGEHSFEKEFKLTSAIKKELNERLPNYMIPRKFMYQSSIPMTPNGKVDRKKLLSEVTA 504
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...eeee...........eeeehhhhhhhhhhh.....hhhhh.....eeeeeee..----.eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhh..............eeee.....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhhhhh.....eee....eeeee............eeeeee..........hhhhhhhheeee..eeeeeeeeeeeee..eeeeeee.hhheee..eeehhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhh..hhhhh..eeee............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fce A   1 MKLLEQIEKWAAETPDQTAFVWRDAKITYKQLKEDSDALAHWISSEYPDDRSPIMVYGHMQPEMIINFLGCVKAGHAYIPVDLSIPADRVQRIAENSGAKLLLSATAVTVTDLPVRIVSEDNLKDIFFTHKGNTPNPEHAVKGDENFYIIYTSG----PKGVQITYNCLVSFTKWAVEDFNLQTGQVFLNQAPFSFDLSVMDIYPSLVTGGTLWAIDKDMIARPKDLFASLEQSDIQVWTSTPSFAEMCLMEASFSESMLPNMKTFLFCGEVLPNEVARKLIERFPKATIMNTYGPTEATVAVTGIHVTEEVLDQYKSLPVGYCKSDCRLLIMKEDGTIAPDGEKGEIVIVGPSVSVGYLGSPELTEKAFTMIDGERAYKTGDAGYVENGLLFYNGRLDFQIKLHGYRMELEEIEHHLRACSYVEGAVIVPIKKGEKYDYLLAVVVPGEHSFEKEFKLTSAIKKELNERLPNYMIPRKFMYQSSIPMTPNGKVDRKKLLSEVTA 504
                                    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       500    
                                                                                                                                                                                   154  159
   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  (0, 0)

(no "SCOP Domain" information available for 3FCE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FCE)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DLTA_BACCR | Q81G39)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047473    D-alanine-poly(phosphoribitol) ligase activity    Catalysis of the reaction: poly(ribitol phosphate) + D-alanine + ATP = O-D-alanyl-poly(ribitol phosphate) + diphosphate + AMP.
    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:0016876    ligase activity, forming aminoacyl-tRNA and related compounds    Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
    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:0070395    lipoteichoic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipoteichoic acid, which is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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
        DLTA_BACCR | Q81G39: 3dhv 3fcc 4pzp

(-) Related Entries Specified in the PDB File

3dhv CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH D-ALANINE ADENYLATE
3fcc CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH ATP AND MAGNESIUM