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(-) Description

Title :  PUTATIVE ATP-DEPENDENT DNA LIGASE FROM AQUIFEX AEOLICUS.
 
Authors :  J. Osipiuk, P. Quartey, F. Collart, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  28 Feb 11  (Deposition) - 16 Mar 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, P. Quartey, F. Collart, A. Joachimiak
Putative Atp-Dependent Dna Ligase From Aquifex Aeolicus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AQ_1106
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Strain: VF5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2CA2Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:51 , GLU A:75 , GLU A:76 , LYS A:77 , VAL A:78 , ASN A:82 , ARG A:97 , GLU A:129 , PHE A:154 , VAL A:182 , VAL A:214 , LYS A:216 , HOH A:375BINDING SITE FOR RESIDUE ADN A 501
2AC2SOFTWARETYR B:51 , ILE B:54 , GLU B:75 , GLU B:76 , LYS B:77 , VAL B:78 , ASN B:82 , ARG B:97 , GLU B:129 , PHE B:154 , VAL B:182 , VAL B:214 , LYS B:216BINDING SITE FOR RESIDUE ADN B 501
3AC3SOFTWAREASP A:79 , GLU A:140 , ASP A:236 , HOH A:398 , HOH A:410BINDING SITE FOR RESIDUE CA A 601
4AC4SOFTWAREASP B:79 , GLU B:140 , ASP B:236 , HOH B:412BINDING SITE FOR RESIDUE CA B 602
5AC5SOFTWAREGLU A:76 , VAL A:78 , PHE A:152 , HIS A:181 , VAL A:182 , GLU A:183 , ARG A:210 , GLU B:207BINDING SITE FOR RESIDUE GOL A 603
6AC6SOFTWAREGLU B:76 , TYR B:144 , PHE B:152 , HIS B:181 , VAL B:182 , GLU B:183BINDING SITE FOR RESIDUE GOL B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QWU)

(-) Exons   (0, 0)

(no "Exon" information available for 3QWU)

(-) 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:366
 aligned with O67191_AQUAE | O67191 from UniProtKB/TrEMBL  Length:367

    Alignment length:366
                                    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      
         O67191_AQUAE     2 ISPELVKEALKKKKVRSEEAFGLEYLRFNDDYKDIPRGTAIFKDFIIWGYPHIGRIFLLETGLREQFEAPFWVEEKVDGYNTRIFKYGDNYYALSRGGFICPFTTDRLPDLIDLRILDENPDLVICAEVAGPENPYIEESPPYVKEDVQLFVFDFMKKNEQGFLSQEEKMELIEKYNLPHVEILGRFTASEEGIKKIKEILKRFNEEGREGVVFKEDSERNKRAKYITSYANLMDIKTNAKNMLQLPPEYYTNRILRLVLFMYEEGLKTTEHLYEELGRAFIDGLFQAIEQFEKEHKVYKTFTCKFRKKENAIALLELLSKTSKHIQVKERRLEKEGDYWRLEFDKVFLNMTGLLGHLLSGGIVYD 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh..eeeeee..eeeeee...........ee....ee......eee.hhhhhhhhhh...eeeeee...eeeeeeee..eeeee......hhhhhhhhhhhh.hhhhhhh..eeeeeeee..................eeeeeeeee.......hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh...eeeeee......eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qwu A   2 ISPELVKEALKKKKVRSEEAFGLEYLRFNDDYKDIPRGTAIFKDFIIWGYPHIGRIFLLETGLREQFEAPFWVEEKVDGYNTRIFKYGDNYYALSRGGFICPFTTDRLPDLIDLRILDENPDLVICAEVAGPENPYIEESPPYVKEDVQLFVFDFMKKNEQGFLSQEEKMELIEKYNLPHVEILGRFTASEEGIKKIKEILKRFNEEGREGVVFKEDSERNKRAKYITSYANLMDIKTNAKNMLQLPPEYYTNRILRLVLFMYEEGLKTTEHLYEELGRAFIDGLFQAIEQFEKEHKVYKTFTCKFRKKENAIALLELLSKTSKHIQVKERRLEKEGDYWRLEFDKVFLNMTGLLGHLLSGGIVYD 367
                                    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      


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with O67191_AQUAE | O67191 from UniProtKB/TrEMBL  Length:367

    Alignment length:364
                                    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       352       362    
         O67191_AQUAE     3 SPELVKEALKKKKVRSEEAFGLEYLRFNDDYKDIPRGTAIFKDFIIWGYPHIGRIFLLETGLREQFEAPFWVEEKVDGYNTRIFKYGDNYYALSRGGFICPFTTDRLPDLIDLRILDENPDLVICAEVAGPENPYIEESPPYVKEDVQLFVFDFMKKNEQGFLSQEEKMELIEKYNLPHVEILGRFTASEEGIKKIKEILKRFNEEGREGVVFKEDSERNKRAKYITSYANLMDIKTNAKNMLQLPPEYYTNRILRLVLFMYEEGLKTTEHLYEELGRAFIDGLFQAIEQFEKEHKVYKTFTCKFRKKENAIALLELLSKTSKHIQVKERRLEKEGDYWRLEFDKVFLNMTGLLGHLLSGGIVY 366
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------DNA_ligase_A_M-3qwuB01 B:58-235                                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------DNA_ligase_A_M-3qwuB02 B:58-235                                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh..eeeeee..eeeeee...........ee....ee......eee.hhhhhhhhhh...eeeeee...eeeeeeee..eeeee......hhhhhhhhhhhh.hhhhhhh..eeeeeeee..................eeeeeeeee.......hhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhh...eeeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qwu B   3 SPELVKEALKKKKVRSEEAFGLEYLRFNDDYKDIPRGTAIFKDFIIWGYPHIGRIFLLETGLREQFEAPFWVEEKVDGYNTRIFKYGDNYYALSRGGFICPFTTDRLPDLIDLRILDENPDLVICAEVAGPENPYIEESPPYVKEDVQLFVFDFMKKNEQGFLSQEEKMELIEKYNLPHVEILGRFTASEEGIKKIKEILKRFNEEGREGVVFKEDSERNKRAKYITSYANLMDIKTNAKNMLQLPPEYYTNRILRLVLFMYEEGLKTTEHLYEELGRAFIDGLFQAIEQFEKEHKVYKTFTCKFRKKENAIALLELLSKTSKHIQVKERRLEKEGDYWRLEFDKVFLNMTGLLGHLLSGGIVY 366
                                    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       352       362
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DNA_ligase (17)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O67191_AQUAE | O67191)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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