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(-) Description

Title :  TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA
 
Authors :  M. Deibert, S. Grazulis, G. Sasnauskas, V. Siksnys, R. Huber
Date :  07 Aug 00  (Deposition) - 07 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Protein-Dna Complex, Double Helix, Restriction Endonuclease, Restriction-Modifiction Systems, Hydrolase, Phosphodiesterase, Metal Ion, Complex (Endonuclease/Dna), Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Deibert, S. Grazulis, G. Sasnauskas, V. Siksnys, R. Huber
Structure Of The Tetrameric Restriction Endonuclease Ngomiv In Complex With Cleaved Dna.
Nat. Struct. Biol. V. 7 792 2000
PubMed-ID: 10966652  |  Reference-DOI: 10.1038/79032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*GP*CP*G)-3')
    ChainsE, F, G, H
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3')
    ChainsI, J, K, L
    EngineeredYES
    SyntheticYES
 
Molecule 3 - TYPE II RESTRICTION ENZYME NGOMI
    ChainsA, B, C, D
    EC Number3.1.21.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificNEISSERIA GONORRHOEAE
    Organism Taxid485
    SynonymNGOMIV RESTRICTION ENDONUCLEASE, ENDONUCLEASE NGOMI, R.NGOMI

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2MG8Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:140 , ACY B:3002 , MG B:3333 , HOH B:3345 , HOH B:3403 , DC I:5 , HOH I:259BINDING SITE FOR RESIDUE MG I 2222
02AC2SOFTWAREASP A:140 , ACY A:2001 , MG A:5555 , HOH A:5562 , HOH A:5593 , HOH F:22 , DC J:5BINDING SITE FOR RESIDUE MG J 4444
03AC3SOFTWAREASP C:140 , ACY C:4003 , MG C:7777 , HOH C:7779 , HOH C:7780 , DC K:5 , HOH K:271BINDING SITE FOR RESIDUE MG K 6666
04AC4SOFTWAREASP D:140 , HOH D:1026 , HOH D:1109 , HOH D:1118 , ACY D:5004 , MG D:9999 , DC L:5BINDING SITE FOR RESIDUE MG L 8888
05AC5SOFTWAREASP A:140 , CYS A:186 , ACY A:2001 , HOH A:5564 , DC J:5 , HOH J:221 , MG J:4444BINDING SITE FOR RESIDUE MG A 5555
06AC6SOFTWAREASP A:140 , SER A:185 , CYS A:186 , LYS A:187 , ASN A:197 , ALA A:198 , MG A:5555 , HOH A:5562 , HOH A:5593 , DC J:5 , HOH J:221 , MG J:4444BINDING SITE FOR RESIDUE ACY A 2001
07AC7SOFTWAREASP B:140 , CYS B:186 , ACY B:3002 , HOH B:3390 , DC I:5 , HOH I:57 , MG I:2222BINDING SITE FOR RESIDUE MG B 3333
08AC8SOFTWAREASP B:140 , SER B:185 , CYS B:186 , LYS B:187 , ASN B:197 , ALA B:198 , MG B:3333 , HOH B:3384 , HOH B:3403 , DC I:5 , HOH I:57 , HOH I:259 , MG I:2222BINDING SITE FOR RESIDUE ACY B 3002
09AC9SOFTWAREASP C:140 , CYS C:186 , ACY C:4003 , HOH C:7781 , DC K:5 , HOH K:328 , MG K:6666BINDING SITE FOR RESIDUE MG C 7777
10BC1SOFTWAREASP C:140 , SER C:185 , CYS C:186 , LYS C:187 , ASN C:197 , ALA C:198 , GLU C:201 , MG C:7777 , HOH C:7780 , HOH C:7829 , DC K:5 , HOH K:271 , HOH K:328 , MG K:6666BINDING SITE FOR RESIDUE ACY C 4003
11BC2SOFTWAREASP D:140 , CYS D:186 , HOH D:1022 , ACY D:5004 , DC L:5 , HOH L:55 , MG L:8888BINDING SITE FOR RESIDUE MG D 9999
12BC3SOFTWAREASP D:140 , SER D:185 , CYS D:186 , LYS D:187 , ASN D:197 , ALA D:198 , HOH D:1020 , HOH D:1026 , HOH D:1109 , MG D:9999 , DC L:5 , HOH L:55 , MG L:8888BINDING SITE FOR RESIDUE ACY D 5004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FIU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FIU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FIU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FIU)

(-) Exons   (0, 0)

(no "Exon" information available for 1FIU)

(-) 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: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 d1fiua_ A: Restriction endonuclease NgoIV                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fiuA00 A:1-286  [code=3.40.50.10010, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh........eeeee...hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fiu 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 d1fiub_ B: Restriction endonuclease NgoIV                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fiuB00 B:1-286  [code=3.40.50.10010, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh........eeeee......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eeeee...hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fiu 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 C 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 d1fiuc_ C: Restriction endonuclease NgoIV                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fiuC00 C:1-286  [code=3.40.50.10010, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh........eeeee.......hhhhhhhhhhhhhhhhhhhhh..hhhhhh........eeeee...hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fiu C   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 D 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 d1fiud_ D: Restriction endonuclease NgoIV                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fiuD00 D:1-286  [code=3.40.50.10010, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhh........................eeeeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fiu D   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:4
                                    
                 1fiu E   1 TGCG   4

Chain F from PDB  Type:DNA  Length:4
                                    
                 1fiu F   1 TGCG   4

Chain G from PDB  Type:DNA  Length:4
                                    
                 1fiu G   1 TGCG   4

Chain H from PDB  Type:DNA  Length:4
                                    
                 1fiu H   1 TGCG   4

Chain I from PDB  Type:DNA  Length:7
                                       
                 1fiu I   5 CCGGCGC  11

Chain J from PDB  Type:DNA  Length:7
                                       
                 1fiu J   5 CCGGCGC  11

Chain K from PDB  Type:DNA  Length:7
                                       
                 1fiu K   5 CCGGCGC  11

Chain L from PDB  Type:DNA  Length:7
                                       
                 1fiu L   5 CCGGCGC  11

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FIU)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (T2M4_NEIGO | P31032)
molecular function
    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.
    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.
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)

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        T2M4_NEIGO | P310324abt

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