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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV WITH COGNATE UNCLEAVED DNA
 
Authors :  E. N. Manakova, S. Grazulis, M. Zaremba, G. Tamulaitiene, D. Golovenko V. Siksnys
Date :  11 Dec 11  (Deposition) - 28 Dec 11  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,E,G
Biol. Unit 1:  A,B,E,G  (2x)
Keywords :  Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Manakova, S. Grazulis, M. Zaremba, G. Tamulaitiene, D. Golovenko, V. Siksnys
Structure Of Type Iif Restriction Endonuclease Ngomiv With Cognate Uncleaved Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE-2 RESTRICTION ENZYME NGOMIV
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HMS 174 DE3
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
    Synonym: TYPE IIF RESTRICTION ENDONUCLEASE NGOMIV, R.NGOMIV, ENDONUCLEASE NGOMIV, TYPE II RESTRICTION ENZYME NGOMIV
 
Molecule 2 - 5'-D(*TP*GP*CP*GP*CP*CP*GP*GP*CP*GP*CP)-3'
    Chains: E, G
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEG
Biological Unit 1 (2x): ABEG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:140 , CYS A:186 , HOH A:2045 , HOH A:2087 , HOH A:2088 , DC E:5BINDING SITE FOR RESIDUE CA A1287
2AC2SOFTWAREASP B:140 , CYS B:186 , HOH B:2041 , HOH B:2060 , HOH B:2074 , DC G:5BINDING SITE FOR RESIDUE CA B1287
3AC3SOFTWAREHOH E:2005 , HOH E:2006 , HOH E:2014BINDING SITE FOR RESIDUE CA E1000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ABT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ABT)

(-) 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:286
 aligned with T2M4_NEIGO | P31032 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:286
                                    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      
           T2M4_NEIGO     1 MNPLFTQERRIFHKKLLDGNILATNNRGVVSNADGSNTRSFNIAKGIADLLHSETVSERLPGQTSGNAFEAICSEFVQSAFEKLQHIRPGDWNVKQVGSRNRLEIARYQQYAHLTALAKAAEENPELAAALGSDYTITPDIIVTRNLIADAEINRNEFLVDENIATYASLRAGNGNMPLLHASISCKWTIRSDRAQNARSEGLNLVRNRKGRLPHIVVVTAEPTPSRISSIALGTGEIDCVYHFALYELEQILQSLNYEDALDLFYIMVNGKRLKDISDLPLDLAV 286
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4abt A   1 MQPLFTQERRIFHKKLLDGNILATNNRGVVSNADGSNTRSFNIAKGIADLLHSETVSERLPGQTSGNAFEAICSEFVQSAFEKLQHIRPGDWNVKQVGSRNRLEIARYQQYAHLTALAKAAEENPELAAALGSDYTITPDIIVTRNLIADAEINRNEFLVDENIATYASLRAGNGNMPLLHASISCKWTIRSDRAQNARSEGLNLVRNRKGRLPHIVVVTAEPTPSRISSIALGTGEIDCVYHFALYELEQILQSLNYEDALDLFYIMVNGKRLKDISDLPLDLAV 286
                                    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      


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with T2M4_NEIGO | P31032 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:286
                                    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      
           T2M4_NEIGO     1 MNPLFTQERRIFHKKLLDGNILATNNRGVVSNADGSNTRSFNIAKGIADLLHSETVSERLPGQTSGNAFEAICSEFVQSAFEKLQHIRPGDWNVKQVGSRNRLEIARYQQYAHLTALAKAAEENPELAAALGSDYTITPDIIVTRNLIADAEINRNEFLVDENIATYASLRAGNGNMPLLHASISCKWTIRSDRAQNARSEGLNLVRNRKGRLPHIVVVTAEPTPSRISSIALGTGEIDCVYHFALYELEQILQSLNYEDALDLFYIMVNGKRLKDISDLPLDLAV 286
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.........eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee...hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4abt B   1 MQPLFTQERRIFHKKLLDGNILATNNRGVVSNADGSNTRSFNIAKGIADLLHSETVSERLPGQTSGNAFEAICSEFVQSAFEKLQHIRPGDWNVKQVGSRNRLEIARYQQYAHLTALAKAAEENPELAAALGSDYTITPDIIVTRNLIADAEINRNEFLVDENIATYASLRAGNGNMPLLHASISCKWTIRSDRAQNARSEGLNLVRNRKGRLPHIVVVTAEPTPSRISSIALGTGEIDCVYHFALYELEQILQSLNYEDALDLFYIMVNGKRLKDISDLPLDLAV 286
                                    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      


Chain E from PDB  Type:DNA  Length:11
                                           
                 4abt E   1 TGCGCCGGCGC  11
                                    10 


Chain G from PDB  Type:DNA  Length:11
                                           
                 4abt G   1 TGCGCCGGCGC  11
                                    10
   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)
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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 4ABT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T2M4_NEIGO | P31032)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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
        T2M4_NEIGO | P31032: 1fiu

(-) Related Entries Specified in the PDB File

1fiu TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITHCLEAVED DNA