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(-) Description

Title :  CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH D-ALANINE ADENYLATE
 
Authors :  L. Du, Y. He, Y. Luo
Date :  18 Jun 08  (Deposition) - 04 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Dlta, Amp-Forming Domain, D-Alanine, Adenylation, D-Alanine Carrier Protein Ligase, Cytoplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Du, Y. He, Y. Luo
Crystal Structure And Enantiomer Selection By D-Alanyl Carrier Protein Ligase Dlta From Bacillus Cereus.
Biochemistry V. 47 11473 2008
PubMed-ID: 18847223  |  Reference-DOI: 10.1021/BI801363B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANINE-POLY(PHOSPHORIBITOL) LIGASE
    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 Vector Type: PLASMID
    Gene: DLTA
    Mutation: YES
    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
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2DAL1Ligand/IonD-ALANINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:196 , ASP A:197 , CYS A:269 , GLY A:270 , GLY A:295 , VAL A:301 , LYS A:492 , AMP A:711BINDING SITE FOR RESIDUE DAL A 701
2AC2SOFTWAREASP A:197 , GLY A:270 , GLU A:271 , VAL A:272 , ASN A:292 , THR A:293 , TYR A:294 , GLY A:295 , THR A:297 , VAL A:321 , ASP A:383 , TYR A:394 , ARG A:397 , LYS A:492 , DAL A:701 , HOH A:833 , HOH A:848BINDING SITE FOR RESIDUE AMP A 711

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3DHV)

(-) 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:498
 aligned with DLTA_BACCR | Q81G39 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:503
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   
           DLTA_BACCR     2 KLLEQIEKWAAETPDQTAFVWRDAKITYKQLKEDSDALAHWISSEYPDDRSPIMVYGHMQPEMIINFLGCVKAGHAYIPVDLSIPADRVQRIAENSGAKLLLSATAVTVTDLPVRIVSEDNLKDIFFTHKGNTPNPEHAVKGDENFYIIYTSGSTGNPKGVQITYNCLVSFTKWAVEDFNLQTGQVFLNQAPFSFDLSVMDIYPSLVTGGTLWAIDKDMIARPKDLFASLEQSDIQVWTSTPSFAEMCLMEASFSESMLPNMKTFLFCGEVLPNEVARKLIERFPKATIMNTYGPTEATVAVTGIHVTEEVLDQYKSLPVGYCKSDCRLLIMKEDGTIAPDGEKGEIVIVGPSVSVGYLGSPELTEKAFTMIDGERAYKTGDAGYVENGLLFYNGRLDFQIKLHGYRMELEEIEHHLRACSYVEGAVIVPIKKGEKYDYLLAVVVPGEHSFEKEFKLTSAIKKELNERLPNYMIPRKFMYQSSIPMTPNGKVDRKKLLSEVTA 504
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh..eeee...........eeeehhhhhhhhhhh.....hhhhh.....eeeeeee.-----.eeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhh.............eeee.....hhhhhhhhhhhh...eeeeee.hhhhh...eeee.hhhhhhhh.....eee....eeeee............eeeeee..........hhhhhhhheeee..eeeeeeeeeeeee..eeeeeee...eee....eeehhhhhhhhhhh..eeeeeeeeee....eeeeeeeeee......hhhhhhhhhhhhhhh..hhhhh..eeee............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dhv A   2 KLLEQIEKWAAETPDQTAFVWRDAKITYKQLKEDSDALAHWISSEYPDDRSPIMVYGHMQPEMIINFLGCVKAGHAYIPVDLSIPADRVQRIAENSGAKLLLSATAVTVTDLPVRIVSEDNLKDIFFTHKGNTPNPEHAVKGDENFYIIYTS-----PKGVQITYNCLVSFTKWAVEDFNLQTGQVFLNQAPFSFDLSVMDIYPSLVTGGTLWAIDKDMIARPKDLFASLEQSDIQVWTSTPSFAEMCLMEASFSESMLPNMKTFLFCGEVLPNEVARKLIERFPKATIMNTYGPTEATVAVTGIHVTEEVLDQYKSLPVGYCKSDCRLLIMKEDGTIAPDGEKGEIVIVGPSVSVGYLGSPELTEKAFTMIDGERAYKTGDAGYVENGLLFYNGRLDFQIKLHGYRMELEEIEHHLRACSYVEGAVIVPIKKGEKYDYLLAVVVPGEHSFEKEFKLTSAIKKELNERLPNYMIPRKFMYQSSIPMTPNGKVDRKKLLSEVTA 504
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 |     161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   
                                                                                                                                                                                 153   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 3DHV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  3dhv
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  DLTA_BACCR | Q81G39
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DLTA_BACCR | Q81G39: 3fcc 3fce 4pzp

(-) Related Entries Specified in the PDB File

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