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(-) Description

Title :  RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP
 
Authors :  M. E. Marsh, M. T. Ehebauer, D. Scott, C. Abell, T. L. Blundell, M. Hyvone
Date :  24 Jun 14  (Deposition) - 14 Jan 15  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Rada, Recombinase, Atpase, Adp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Marsh, D. E. Scott, M. T. Ehebauer, C. Abell, T. L. Blundell, M. Hyvonen
Atp Half-Sites In Rada And Rad51 Recombinases Bind Nucleotides
Febs Open Bio V. 6 372 2016
PubMed-ID: 27419043  |  Reference-DOI: 10.1002/2211-5463.12052

(-) Compounds

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAT4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-349
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: RADA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:139 , PHE B:140 , GLY B:141 , SER B:142 , GLY B:143 , LYS B:144 , THR B:145 , GLN B:146 , ARG B:181 , GLN B:284 , ARG B:323 , ILE B:342 , MG B:1351 , HOH B:2042 , HOH B:2043 , HOH B:2044 , HOH B:2096 , HOH B:2100 , HOH B:2101 , HOH B:2195 , HOH B:2224 , HOH B:2233 , HOH B:2236BINDING SITE FOR RESIDUE ADP B1350
2AC2SOFTWARETHR B:145 , ADP B:1350 , HOH B:2041 , HOH B:2042 , HOH B:2043 , HOH B:2195BINDING SITE FOR RESIDUE MG B1351
3AC3SOFTWAREPHE A:140 , GLY A:141 , SER A:142 , GLY A:143 , LYS A:144 , THR A:145 , GLN A:146 , ARG A:181 , GLN A:284 , ARG A:323 , ILE A:342 , MG A:1351 , HOH A:2041 , HOH A:2043 , HOH A:2045 , HOH A:2101 , HOH A:2102 , HOH A:2110 , HOH A:2218 , HOH A:2234 , HOH A:2247 , HOH A:2256 , HOH A:2257BINDING SITE FOR RESIDUE ADP A1350
4AC4SOFTWARETHR A:145 , ADP A:1350 , HOH A:2041 , HOH A:2042 , HOH A:2043 , HOH A:2218BINDING SITE FOR RESIDUE MG A1351
5AC5SOFTWAREGLY A:111 , ARG A:112 , LEU A:164 , HOH A:2260BINDING SITE FOR RESIDUE NA A1352
6AC6SOFTWAREMET B:212 , VAL B:215 , HIS B:264 , ASP B:267BINDING SITE FOR RESIDUE NA B1352
7AC7SOFTWAREPHE B:206 , ARG B:316 , GLY B:318 , LYS B:319BINDING SITE FOR RESIDUE NA B1353

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UQO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:238 -Ser A:239
2Asp B:238 -Ser B:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UQO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UQO)

(-) Exons   (0, 0)

(no "Exon" information available for 4UQO)

(-) Sequences/Alignments

Asymmetric 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eeeeeee.hhh.eeeeee.........eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uqo A 108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       307       317       327       337       347  
                                                                                                                                                                                                            286|                                          
                                                                                                                                                                                                             307                                          


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...hhhhhhhhh..ee..eeeeeee....hhhhhhhhhhhhh..hhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhh.hhhhhhhhhhhh.....eeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.hhh.eeeeee.........eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uqo B 108 ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVLAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED 349
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       306       316       326       336       346   
                                                                                                                                                                                                           285|                                            
                                                                                                                                                                                                            305
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  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 4UQO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UQO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UQO)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RADA_PYRFU | O74036: 1pzn 4a6p 4a6x 4b2i 4b2l 4b2p 4b32 4b33 4b34 4b35 4b3b 4b3c 4b3d 4d6p 5fos 5fot 5fou 5fov 5fow 5fox 5fpk 5j4h 5j4k 5j4l 5jec 5jed 5jee 5jfg 5kdd 5l8v 5lb2 5lb4 5lbi

(-) Related Entries Specified in the PDB File

4upi DIMERIC SULFATASE SPAS1 FROM SILICIBACTER POMEROYI
4upk PHOSPHONATE MONOESTER HYDROLASE SPPMH FROM SILICIBACTER POMEROYI
4upl DIMERIC SULFATASE SPAS2 FROM SILICIBACTER POMEROYI