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(-) Description

Title :  STRUCTURE OF A NUCLEASE-DELETION MUTANT OF THE TYPE ISP RESTRICTION-MODIFICATION ENZYME LLAGI IN COMPLEX WITH A DNA SUBSTRATE MIMIC
 
Authors :  K. Saikrishnan, M. Kulkarni, N. Nirwan
Date :  18 Dec 15  (Deposition) - 30 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Helicase-Like Atpase, Methyltransferase, Dna-Binding Protein, Restriction-Modification Enzyme, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kulkarni, N. Nirwan, K. Van Aelst, M. D. Szczelkun, K. Saikrishnan
Structural Insights Into Dna Sequence Recognition By Type Isp Restriction-Modification Enzymes
Nucleic Acids Res. V. 44 4396 2016
PubMed-ID: 26975655  |  Reference-DOI: 10.1093/NAR/GKW154

(-) Compounds

Molecule 1 - ENDONUCLEASE AND METHYLASE LLAGI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 166-1570
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
 
Molecule 2 - DNA (5'- D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T) -3')
    Chains: D, E
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G) -3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FFJ)

(-) Sites  (0, 0)

(no "Site" information available for 5FFJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FFJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:226 -Pro B:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FFJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FFJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5FFJ)

(-) 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:1044
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh...eeeeee..hhhhh.............hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhh.....eeeee....hhhhh...........eeeee....................eee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...........eee.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhh........eee.hhhhhh.......hhhhhhhhhh.......eeee...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeee......hhhhhhhh...hhhhh...eeeeeeee......eeeeee.....hhhhhhhhhhhh........eee..............hhhhhee............ee.....hhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.........hhhhhhhhhh......hhh.eeeeeee..eeeeee..........hhhhhh........eeeee.........eeee..ee.hhhh...eeeee.ee......ee...hhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhh..........eeee....................ee....eeee..hhhhhh.ee..eehhhhhhhhh..ee......eehhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5ffj A  176 KKLRDYQQTAKENALAHFKENDRGQLIMAPGTGKTFTSLKISEALSKDKNGPFKVLYLVPSIQLLTQTLRGWNNDTELTITSMAVTSDRDASRGKASDIGYPATTSSKKILQNWHDFESLPKQTDMLVVFSTYQSIEVIGEAQKEGFPEFDFIISDEAHRSAFSKVHSNNNVKGLKRMYQTATPKIYILLSSMDDESKYGEVFFRMGFGQAVSRDINWSKDVAKIAERQINWIKNKLSKDPISLEFKKFVSSLQHNINDSIDEKQAAEMLSQHLITKPIFEALFSEYSFVNQNPVSQAMESIVSELEKAGFAKEQENLEPLYESVRMRAEGIEDKQKIIVTLYDKFFKTAFKIVFTPIEVVDFIVHSVDDVLKKHFGKSLASKDVHILDPFTGTGTFIVRTLTYLKEQMDAGEISLSDITRKFMKELHANEIVLLSYYIAAINIEATFDEIYVPFEGIVLTDTFESTETEEDDYFGTNDERLKRQQEVPITAIIGNPPYSKGQSNENDNNKNIEYPRLFKSIADSYVKNSKTTSVLGMYDSYVLSIRWASNRLNDKGVIGFVSNGSYIDSQSADGLRKSLFKEFNHLYIFNLRGDQRTQGETSRKEGGKIFGSGSRTSIAISILVKDDSDNHEVHYHDIGDYLTRDDKLDILRDKESILNIDWENISPDENNDWINQRDQNYLNYRPLADENGSIFSVKDIGIVTNRDAWVSNFSKINVSDNVQIMIKNYNLEVDRLENIDVKLNDKTVVDYVTNDERKISWSRSLKQRAARREKTQFSHSDIMLAMYRPFTKKYLYRNRFLNENVRKTYQTFPDKNSKNLLINISGQGDKADFATLISEYLSDMHVIGGQARNLPRFTYETDGRTDNIVSDDEFYYVYGVLHSSAYRKRYANDLKKDLPRIPLLKNKDKYVEIGRKLSDLHLNYENQPIWDGIEVEISQPDYRVKKMKHPKKGVLDTIIYNESITIKNIPERAYEYVVNGRPAIEWIIDQYQVKTDKKSGITDDPNEFSDNPKYILNLLLSVITVSMRTLELIEELPEFEIQE 1570
                                   185       195       205       215       225       235       245       255       265   ||  282       292       302       312       322       332       342|      363       373      |395       405       415     ||721       731       743       753       763       773       783       793       803       813       823       833 ||    846       856 ||    873       883       893       903       913       923       933       943       953       963||     979       989||    1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382  ||  1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566    
                                                                                                                       269|                                                              342|                       380|                         421|                  739|                                                                                          835|                858|                                                                                               964|                990|                                                                                                                                                                                                                                                                                                                                                                                                   1385|                                                                                                                                                                                    
                                                                                                                        277                                                               354                        393                          718                   742                                                                                           839                 866                                                                                                971                 994                                                                                                                                                                                                                                                                                                                                                                                                    1390                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:1232
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh....eeeeee..hhhhh..........hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhh....eeeeeee.hhhh........hhhhh.....eeeeeee.....ee...ee..........eeeeeehhhhhhhh.......ee..hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh................eeee.....hhhhhhhhhhh........ee......hhhhhhhhhhhhhhhhhh.hhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh...........eee.hhhhhh..........hhhhhhhhhhhhh..eeeeee...................hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhheeeeeeeeeeee.hhhh...hhhhhhhhhhhh.eeeeeeee......hhhhhhhh...........eeeeeee.......eeeeee.....hhhhhhhhhhhhh.......eee............hhhhhhhee............ee.....hhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.........hhhhhhhhhh..........eeeeeee..eeeeee........................eeee..........eeee..ee.........eeee.ee....ee...hhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhh..........eeee...................ee.....eeee..hhhhhh.ee..eehhhhhhhhh..ee......eehhhhh....hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ffj B  178 LRDYQQTAKENALAHFKENDRGQLIMAPGTGKTFTSLKISEALSKDKNGPFKVLYLVPSIQLLTQTLRGWNNDTELTITSMAVTSDRDASASDIGYPATTSSKKILQNWHDFESLPKQTDMLVVFSTYQSIEVIGEAQKEGFPEFDFIISDEAHRTTGAHASAFSKVHSNNNVKGLKRMYQTATPKIYGSILLSSMDDESKYGEVFFRMGFGQAVSRDILTDYKVMVRIVGIWNGMMRRRAIAFTRTIEESKKVSSQFEEVVNEYLSMRHNALQKGEILDWLADPNKPADIVSDIPTLDAVIFLSPKKSQVDIVQAVGRIMRKDYGYIILPIVINNKNYETVWQVINALRSVDERFEAMIDKLNMAKQLKVWNKFEGAIFGKIVQKVGDRKYLENWSKDVAKIAERQINWIKNKLSDKKDPISLEFKKFVSSLQHNINDSIDEKQAAEMLSQHLITKPIFEALFSEYSFVNQNPVSQAMESIVSELEKAGFAKEQENLEPLYESVRMRAEGIEKAEDKQKIIVTLYDKFFKTAFIVFTPIEVVDFIVHSVDDVLKKHFGKSLASKDVHILDPFTGTGTFIVRTLTYLKEQMDAGEISLSDITRKFMKELHANEIVLLSYYIAAINIEATFDEINGEEEGYVPFEGIVLTDTFESTETEETLDDDYFGTNDERLKRQQEVPITAIIGNPPYSKGQSNENDNNKNIEYPRLFKSIADSYVKNSKTTSVLGMYDSYVLSIRWASNRLNDKGVIGFVSNGSYIDSQSADGLRKSLFKEFNHLYIFNLRGDQRTQGETSRKEGGKIFGSGSRTSIAISILVKDDSDNHEVHYHDIGDYLTRDDKLDILRDKESILNIDWENISPDENNDWINQRDQNYLNYRPLADENGSIFSVKDIGIVTNRDAWVSNFSKINVSDNVQIMIKNYNLEVDRLENIDVKLNDKTVVDYVTNDERKISWSRSLKQRAARREKTQFSHSDIMLAMYRPFTKKYLYRNRFLNENVRKTYQTFPDKNSKNLLINISGQGDKADFATLISEYLSDMHVIGGQARNLPRFTYEGRTDNIVSDDEFYYVYGVLHSSAYRKRYANDLKKDLPRIPLLKNKDKYVEIGRKLSDLHLNYENQPIWDGIEVEISQPDYRVKKMKHPKKGVLDTIIYNESITIKNIPERAYEYVVNGRPAIEWIIDQYQVKTDKKSGITDDPNEFSDNPKYILNLLLSVITVSMRTLELIEELPEFEIQ 1569
                                   187       197       207       217       227       237       247       257       267|      287       297       307       317       327       337       347|      362       372       392       402       412       422      |461       489       499       509    || 530|      545       555| ||   577       587       597  ||   611   ||  632       642       652      |664||     703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853   ||  871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381 ||   1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567  
                                                                                                                   267|                                                                  347|                         381|                                  429|        470|                      514| 530|                555| ||                          600|       615|                             659|  ||                                                                                                                                                               857|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1383|                                                                                                                                                                                   
                                                                                                                    278                                                                   353                          392                                   459         489                       526  536                 559 ||                           605        627                              662  ||                                                                                                                                                                866                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  1390                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                              561|                                                                          665|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                               571                                                                           695                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:DNA  Length:22
                                                       
                5ffj C    2 TAGCTAATAGACTGGATGGAGG   23
                                    11        21  


Chain D from PDB  Type:DNA  Length:22
                                                       
                5ffj D    1 TCCTCCATCCAGTCTATTAGCT   22
                                    10        20  


Chain E from PDB  Type:DNA  Length:23
                                                        
                5ffj E    1 TCCTCCATCCAGTCTATTAGCTA   23
                                    10        20   


Chain F from PDB  Type:DNA  Length:22
                                                       
                5ffj F    2 TAGCTAATAGACTGGATGGAGG   23
                                    11        21
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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

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(no "SCOP Domain" information available for 5FFJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FFJ)

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(no "Pfam Domain" information available for 5FFJ)

(-) Gene Ontology  (12, 12)

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    Gly B:226 - Pro B:227   [ RasMol ]  
 
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4xqk HOMOLOGOUS PROTEIN