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(-) Description

Title :  STRUCTURE OF TYPE IIL RESTRICTION-MODIFICATION ENZYME MMEI IN COMPLEX WITH DNA HAS IMPLICATIONS FOR ENGINEERING OF NEW SPECIFICITIES
 
Authors :  S. J. Callahan, Y. A. Luyten, Y. K. Gupta, G. G. Wilson, R. J. Roberts, R. D A. K. Aggarwal
Date :  22 Jan 16  (Deposition) - 27 Apr 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  C,H,I,J,K,L
Biol. Unit 1:  C,H,I  (1x)
Biol. Unit 2:  J,K,L  (1x)
Keywords :  Dna-Protein Complex, Restriction-Modification Enzyme, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Callahan, Y. A. Luyten, Y. K. Gupta, G. G. Wilson, R. J. Roberts, R. D. Morgan, A. K. Aggarwal
Structure Of Type Iil Restriction-Modification Enzyme Mmei In Complex With Dna Has Implications For Engineering New Specificities.
Plos Biol. V. 14 02442 2016
PubMed-ID: 27082731  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1002442

(-) Compounds

Molecule 1 - MMEI
    Chains: C, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MMEIRM
    Organism Scientific: METHYLOPHILUS METHYLOTROPHUS
    Organism Taxid: 17
 
Molecule 2 - DNA (5'-D(P*TP*AP*TP*CP*CP*GP*AP*CP*AP*TP*AP*AP*C)-3')
    Chains: H, K
    Engineered: YES
    Organism Scientific: METHYLOPHILUS METHYLOTROPHUS
    Organism Taxid: 17
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*TP*TP*AP*TP*GP*TP*CP*GP*GP*AP*TP*A)-3')
    Chains: I, L
    Engineered: YES
    Organism Scientific: METHYLOPHILUS METHYLOTROPHUS
    Organism Taxid: 17
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : CHIJKL
Biological Unit 1 (1x): CHI   
Biological Unit 2 (1x):    JKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2SFG2Ligand/IonSINEFUNGIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SFG1Ligand/IonSINEFUNGIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SFG1Ligand/IonSINEFUNGIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN C:158 , ASP C:201 , CYS C:283 , LEU C:285 , HOH C:1119binding site for residue CA C 1001
2AC2SOFTWAREPHE C:299 , LEU C:311 , GLY C:312 , HIS C:314 , TYR C:315 , THR C:316 , ALA C:363 , CYS C:364 , GLY C:365 , CYS C:366 , ASN C:368 , PHE C:369 , GLU C:413 , ILE C:414 , ASN C:460 , ALA C:461 , ASN C:481 , PRO C:483 , TRP C:517 , HOH C:1111 , DA H:7binding site for residue SFG C 1002
3AC3SOFTWAREGLN J:158 , ASP J:201 , CYS J:283 , LEU J:285 , HOH J:1122 , HOH J:1125binding site for residue CA J 1001
4AC4SOFTWAREPHE J:299 , LEU J:311 , GLY J:312 , HIS J:314 , TYR J:315 , THR J:316 , ALA J:363 , CYS J:364 , GLY J:365 , CYS J:366 , GLY J:367 , ASN J:368 , PHE J:369 , GLU J:413 , ILE J:414 , ASN J:460 , ALA J:461 , ASN J:481 , PRO J:483 , TRP J:517 , DA K:7binding site for residue SFG J 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HR4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile C:448 -Pro C:449
2Ile J:448 -Pro J:449

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HR4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HR4)

(-) Exons   (0, 0)

(no "Exon" information available for 5HR4)

(-) 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 C from PDB  Type:PROTEIN  Length:749
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhh........hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..hhh.eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeee......hhhhh.hhhhh.eeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeeeee......eeeee........eeeee............................ee..........eeehhhhhhhhhhhhhhhh.eeeeehhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...............eeeee.ee.........eee....ee...eeeee..hhhhhhhhhhhhhhhhhhhhheee..eee.....hhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hr4 C 157 PQDPINIKAAERMGKLHDTLKLVGYEGHALELYLVRLLFCLFAEDTTIFEKSLFQEYIETKTLEDGSDLAHHINTLFYVLNTPEQKRLKNLDEHLAAFPYINGKLFEEPLPPAQFDKAMREALLDLCSLDWSRISPAIFGSLFQSIMDAKKRRNLGAHYTSEANILKLIKPLFLDELWVEFEKVKNNKNKLLAFHKKLRGLTFFDPACGCGNFLVITYRELRLLEIEVLRGLHRGGQQVLDIEHLIQINVDQFFGIEIEEFPAQIAQVALWLTDHQMNMKISDEFGNYFARIPLKSTPHILNANALQIDWNDVLEAKKCCFILGNPPFVGKSKQTPGQKADLLSVFGNLKSASDLDLVAAWYPKAAHYIQTNANIRCAFVSTNSITQGEQVSLLWPLLLSLGIKINFAHRTFSWTNEASGVAAVHCVIIGFGLKDSDEKIIYEYESINGEPLAIKAKNINPYLRDGVDVIACKRQQPISKLPSMRYGNKPTDDGNFLFTDEEKNQFITNEPSSEKYFRRFVGGDEFINNTSRWCLWLDGADISEIRAMPLVLARIKKVQEFRLKSSAKPTRQSASTPMKFFYISQPDTDYLLIPETSSENRQFIPIGFVDRNVISSNATYHIPSAEPLIFGLLSSTMHNCWMRNVGGRLESRYRYSASLVYNTFPWIQPNEKQSKAIEEAAFAILKARSNYPNESLAGLYDPKTMPSELLKAHQKLDKAVDSVYGFKGPNTEIARIAFLFETYQKMTSL 905
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896         


Chain H from PDB  Type:DNA  Length:13
                                             
                 5hr4 H   1 TATCCGACATAAC  13
                                    10   


Chain I from PDB  Type:DNA  Length:13
                                             
                 5hr4 I  17 GTTATGTCGGATA  29
                                    26   


Chain J from PDB  Type:PROTEIN  Length:751
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhh........hhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..hhh.eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeee......hhhhh.hhhhh.eeee..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeeeee......eeeee........eeeee............................ee..........eehhhhhhhhhhhhhhhhh.eeeeehhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...............eeeee.ee.........eee....ee...eeeee..hhhhhhhhhhhhhhhhhhhhheee..eee.....hhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hr4 J 156 KPQDPINIKAAERMGKLHDTLKLVGYEGHALELYLVRLLFCLFAEDTTIFEKSLFQEYIETKTLEDGSDLAHHINTLFYVLNTPEQKRLKNLDEHLAAFPYINGKLFEEPLPPAQFDKAMREALLDLCSLDWSRISPAIFGSLFQSIMDAKKRRNLGAHYTSEANILKLIKPLFLDELWVEFEKVKNNKNKLLAFHKKLRGLTFFDPACGCGNFLVITYRELRLLEIEVLRGLHRGGQQVLDIEHLIQINVDQFFGIEIEEFPAQIAQVALWLTDHQMNMKISDEFGNYFARIPLKSTPHILNANALQIDWNDVLEAKKCCFILGNPPFVGKSKQTPGQKADLLSVFGNLKSASDLDLVAAWYPKAAHYIQTNANIRCAFVSTNSITQGEQVSLLWPLLLSLGIKINFAHRTFSWTNEASGVAAVHCVIIGFGLKDSDEKIIYEYESINGEPLAIKAKNINPYLRDGVDVIACKRQQPISKLPSMRYGNKPTDDGNFLFTDEEKNQFITNEPSSEKYFRRFVGGDEFINNTSRWCLWLDGADISEIRAMPLVLARIKKVQEFRLKSSAKPTRQSASTPMKFFYISQPDTDYLLIPETSSENRQFIPIGFVDRNVISSNATYHIPSAEPLIFGLLSSTMHNCWMRNVGGRLESRYRYSASLVYNTFPWIQPNEKQSKAIEEAAFAILKARSNYPNESLAGLYDPKTMPSELLKAHQKLDKAVDSVYGFKGPNTEIARIAFLFETYQKMTSLL 906
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905 


Chain K from PDB  Type:DNA  Length:13
                                             
                 5hr4 K   1 TATCCGACATAAC  13
                                    10   


Chain L from PDB  Type:DNA  Length:12
                                            
                 5hr4 L  18 TTATGTCGGATA  29
                                    27
   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 5HR4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HR4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HR4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5HR4)

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