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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAMERIC RESTRICTION ENDONUCLEASE SFII IN COMPLEX WITH COGNATE DNA (PARTIAL BOUND FORM)
 
Authors :  A. K. Aggarwal, E. S. Vanamee, H Viadiu
Date :  11 Nov 05  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,C,E,F,G,H  (2x)
Biol. Unit 1:  A,C,E,F,G,H  (2x)
Keywords :  Type Iif Restriction Endonuclease, Protein/Dna Complex, Deoxyribonuclease, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Vanamee, H. Viadiu, R. Kucera, L. Dorner, S. Picone, I. Schildkraut, A. K. Aggarwal
A View Of Consecutive Binding Events From Structures Of Tetrameric Endonuclease Sfii Bound To Dna.
Embo J. V. 24 4198 2005
PubMed-ID: 16308566  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600880
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP* TP*T)-3')
    Chains: E, G
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP *AP*T)-3')
    Chains: F, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TYPE II RESTRICTION ENZYME SFII
    Chains: A, C
    EC Number: 3.1.21.4
    Engineered: YES
    Other Details: E.COLI
    Synonym: ENDONUCLEASE SFII, R.SFII
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit (2x): ACEFGH
Biological Unit 1 (2x): ACEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:79 , ASP A:100 , ALA A:101 , DT F:13BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREASP C:100 , ALA C:101 , LYS C:102BINDING SITE FOR RESIDUE CA C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F03)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F03)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F03)

(-) Exons   (0, 0)

(no "Exon" information available for 2F03)

(-) 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:269
 aligned with T2S1_STRFI | O52512 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
           T2S1_STRFI     1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh................eeeeeee......eeeeeeeeeeee.....eeehhhhh...eee........eee......eeeee.....eeeeeeeeeeeeeeeee........eeeeeeeeeee.hhhhhhhhh.......ee.............eeehhhhhhhhh...eeeee..........eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f03 A   1 mHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPmDAEFRNTSSGEVVTmEAGVIPHLmLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130   |   140  |    150       160       170       180       190       200       210       220       230       240       250       260         
                            |                                                                                                                   119-MSE        134-MSE  143-MSE                                                                                                                          
                            1-MSE                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:269
 aligned with T2S1_STRFI | O52512 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
           T2S1_STRFI     1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh................eeeeeee......eeeeeeeeeeee.....eeehhhhh...eeee......eeee......eeeee.....eeeeeeeeeeeeeeeee........eeeeeeeeeee.hhhhhhhhh.......ee.............eeehhhhhhhhh...eeeee..........eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f03 C   1 mHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPmDAEFRNTSSGEVVTmEAGVIPHLmLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130   |   140  |    150       160       170       180       190       200       210       220       230       240       250       260         
                            1-MSE                                                                                                               119-MSE        134-MSE  143-MSE                                                                                                                          


Chain E from PDB  Type:DNA  Length:8
                                        
                 2f03 E   4 TGGCCAAC  11


Chain F from PDB  Type:DNA  Length:7
                                       
                 2f03 F  12 TTGGCCA  18


Chain G from PDB  Type:DNA  Length:5
                                     
                 2f03 G   4 TGGCC   8


Chain H from PDB  Type:DNA  Length:5
                                     
                 2f03 H  14 GGCCA  18
   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 2F03)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F03)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F03)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (T2S1_STRFI | O52512)
molecular function
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        T2S1_STRFI | O52512: 2ezv

(-) Related Entries Specified in the PDB File

2ezv NATIVE COMPLEX