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(-) Description

Title :  STRUCTURE OF THE BFII RESTRICTION ENDONUCLEASE
 
Authors :  S. Grazulis, E. Manakova, M. Roessle, M. Bochtler, G. Tamulaitiene, R. Huber, V. Siksnys
Date :  15 Sep 05  (Deposition) - 07 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bfii, Restriction Endonuclease, Domain Fusion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Grazulis, E. Manakova, M. Roessle, M. Bochtler, G. Tamulaitiene, R. Huber, V. Siksnys
Structure Of The Metal-Independent Restriction Enzyme Bfii Reveals Fusion Of A Specific Dna- Binding Domain With A Nonspecific Nuclease.
Proc. Natl. Acad. Sci. Usa V. 102 15797 2005
PubMed-ID: 16247004  |  Reference-DOI: 10.1073/PNAS.0507949102

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B-BFIIR6, 5
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PET21B
    Organism Scientific: BACILLUS FIRMUS
    Organism Taxid: 1399
    Strain: S8120
    Synonym: BFII RESTRICTION ENDONUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 14)

Asymmetric/Biological Unit (7, 14)
No.NameCountTypeFull Name
1BCT2Ligand/IonBICARBONATE ION
2GOL4Ligand/IonGLYCEROL
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4SRT2Ligand/IonS,R MESO-TARTARIC ACID
5TAR1Ligand/IonD(-)-TARTARIC ACID
6TLA2Ligand/IonL(+)-TARTARIC ACID
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:224 , THR A:225 , GLN A:226 , GLY A:286 , THR A:287 , GLY A:288 , ARG A:291 , GOL A:1359 , HOH A:2247 , HOH A:2252 , HOH A:2253BINDING SITE FOR RESIDUE TAR A1365
02AC2SOFTWAREHIS A:168 , PRO A:178 , HOH A:2254BINDING SITE FOR RESIDUE BCT A1366
03AC3SOFTWAREGLY B:288 , ARG B:291 , TLA B:1363 , HOH B:2225 , HOH B:2226BINDING SITE FOR RESIDUE BCT B1364
04AC4SOFTWAREARG A:100 , LYS A:101 , ARG A:102 , HOH A:2092 , HOH A:2248 , VAL B:199 , SER B:346 , HOH B:2097 , HOH B:2206BINDING SITE FOR RESIDUE TRS A1362
05AC5SOFTWAREPHE A:44 , ASN A:125 , THR A:127 , PRO A:129 , ASN A:134 , HOH A:2108 , HOH A:2249 , HOH A:2250 , SRT B:1362BINDING SITE FOR RESIDUE TLA A1363
06AC6SOFTWARETHR A:174 , ASP A:175 , HOH A:2251 , THR B:75 , PRO B:178 , ASN B:181BINDING SITE FOR RESIDUE SRT A1364
07AC7SOFTWAREPHE A:44 , GLN A:77 , PHE B:44 , ASN B:125 , THR B:127 , PRO B:129 , ASN B:134 , SRT B:1362 , HOH B:2214 , HOH B:2215 , HOH B:2216 , HOH B:2217BINDING SITE FOR RESIDUE MES B1360
08AC8SOFTWAREARG B:82 , GLU B:86 , ASP B:175 , TRP B:180 , HOH B:2126 , HOH B:2127 , HOH B:2218BINDING SITE FOR RESIDUE MES B1361
09AC9SOFTWAREPHE A:44 , HIS A:105 , LYS A:107 , ASN A:125 , TLA A:1363 , PHE B:44 , HIS B:105 , LYS B:107 , ASN B:125 , MES B:1360 , HOH B:2219 , HOH B:2220BINDING SITE FOR RESIDUE SRT B1362
10BC1SOFTWARETHR B:225 , GLN B:226 , GLY B:286 , THR B:287 , GLY B:288 , ARG B:291 , BCT B:1364 , HOH B:2221 , HOH B:2222 , HOH B:2223 , HOH B:2224BINDING SITE FOR RESIDUE TLA B1363
11BC2SOFTWAREGLY A:288 , ARG A:291 , TAR A:1365 , HOH A:2247BINDING SITE FOR RESIDUE GOL A1359
12BC3SOFTWAREHIS A:168 , ASN A:169 , PRO A:178 , GLY A:179BINDING SITE FOR RESIDUE GOL A1360
13BC4SOFTWAREARG A:15 , GLN A:214 , GLY A:294BINDING SITE FOR RESIDUE GOL A1361
14BC5SOFTWAREGLN B:83 , GLU B:86 , GLU B:87 , ASN B:90 , HOH B:2212 , HOH B:2213BINDING SITE FOR RESIDUE GOL B1359

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C1L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:7 -Pro A:8
2His B:7 -Pro B:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C1L)

(-) Exons   (0, 0)

(no "Exon" information available for 2C1L)

(-) 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:358
 aligned with Q9F4C9_BACFI | Q9F4C9 from UniProtKB/TrEMBL  Length:358

    Alignment length:358
                                    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       270       280       290       300       310       320       330       340       350        
         Q9F4C9_BACFI     1 MNFFSLHPNVYATGRPKGLIGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGGRVIAILGGSTSQRLSSRQVVEELLNRGVEVHIINRKRILHAKLYGTSNNLGESLVVSSGNFTGPGMSQNIEASLLLDNNTTQSMGFSWNDMISEMLNQNWHIHNMTNATDASPGWNLLYDERTTNLTLDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....hhhhhhhhhhh........eeeeee...hhhhh..hhhhhhhhhhh..eeeeeee........hhhhhhhhhhh..eeeeee.......eeeeeee..eeeeeee.............eeeeeehhhhhhhhh.hhhhhhhhhh....eeee.......hhhhhhh..........hhhh.eeeeee.hhhhhhhhhh...hhhhh...eeee............ee.......eeeeeeeeee.hhheeeeeeeeeee......eeee.hhhh.........eeeeee....eeeeeee...hhhhhhhhhhh.ee......eeeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1l A   1 MNFFSLHPNVYATGRPKGLIGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGGRVIAILGGSTSQRLSSRQVVEELLNRGVEVHIINRKRILHAKLYGTSNNLGESLVVSSGNFTGPGMSQNIEASLLLDNNTTQSMGFSWNDMISEMLNQNWHIHNMTNATDASPGWNLLYDERTTNLTLDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
                                    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       270       280       290       300       310       320       330       340       350        


Chain B from PDB  Type:PROTEIN  Length:358
 aligned with Q9F4C9_BACFI | Q9F4C9 from UniProtKB/TrEMBL  Length:358

    Alignment length:358
                                    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       270       280       290       300       310       320       330       340       350        
         Q9F4C9_BACFI     1 MNFFSLHPNVYATGRPKGLIGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGGRVIAILGGSTSQRLSSRQVVEELLNRGVEVHIINRKRILHAKLYGTSNNLGESLVVSSGNFTGPGMSQNIEASLLLDNNTTQSMGFSWNDMISEMLNQNWHIHNMTNATDASPGWNLLYDERTTNLTLDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....hhhhhhhhhhh........eeeeee...hhhhh..hhhhhhhhhhh..eeeeeeee......eehhhhhhhhhh..eeeeee.......eeeeeee..eeeeeee....hhhhhh...eeeeeehhhhhhhhh.hhhhhhhhhh....eeee.......hhhhh.ee.........hhhh.eeeeee.hhhhhhhhhh...hhhhh...eeeee...........ee.......eeeeeeeeee.hhheeeeeeeeeee.....eeeee.hhhh.........eeeeeeee..eeeeeee...hhhhhhhhhhh.ee......eeeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1l B   1 MNFFSLHPNVYATGRPKGLIGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGGRVIAILGGSTSQRLSSRQVVEELLNRGVEVHIINRKRILHAKLYGTSNNLGESLVVSSGNFTGPGMSQNIEASLLLDNNTTQSMGFSWNDMISEMLNQNWHIHNMTNATDASPGWNLLYDERTTNLTLDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
                                    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       270       280       290       300       310       320       330       340       350
   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 2C1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C1L)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9F4C9_BACFI | Q9F4C9)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    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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