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(-) Description

Title :  AN ASYMMETRIC COMPLEX OF RESTRICTION ENDONUCLEASE MSPI ON ITS PALINDROMIC DNA RECOGNITION SITE
 
Authors :  Q. S. Xu, R. B. Kucera, R. J. Roberts, H. C. Guo
Date :  06 Feb 04  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Protein-Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. S. Xu, R. B. Kucera, R. J. Roberts, H. C. Guo
An Asymmetric Complex Of Restriction Endonuclease Mspi On Its Palindromic Dna Recognition Site.
Structure V. 12 1741 2004
PubMed-ID: 15341737  |  Reference-DOI: 10.1016/J.STR.2004.07.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'
    Chains: C, D, E, F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TYPE II RESTRICTION ENZYME MSPI
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCAD39
    Expression System Strain: ER2502
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MSPIR
    Organism Scientific: MORAXELLA SP.
    Organism Taxid: 479
    Synonym: ENDONUCLEASE MSPI, R.MSPI

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:35 , ASP A:84 , ASP A:99 , HOH A:546 , HOH A:573BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREGLU B:35 , ASP B:84 , ASP B:99 , HOH B:419 , HOH B:448BINDING SITE FOR RESIDUE NA B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SA3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SA3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SA3)

(-) Exons   (0, 0)

(no "Exon" information available for 1SA3)

(-) 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:262
 aligned with T2M1_MORSP | P11405 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           T2M1_MORSP     1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
               SCOP domains d1sa3a_ A: Restriction endonuclease MspI                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh..hhh.eeeeeeee...............eeeeeee....eeeeeeeeeee....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh.............eeeeeeee..eeeeeeeeehhhhhhhhhhhhhh..hhhhhh..eeee........eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sa3 A   1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
                                    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  


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with T2M1_MORSP | P11405 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           T2M1_MORSP     1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
               SCOP domains d1sa3b_ B: Restriction endonuclease MspI                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Endonuc-MspI-1sa3B01 B:2-262                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -Endonuc-MspI-1sa3B02 B:2-262                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh.hhh.eeeeeeee...............eeeeeee....eeeeeeeeeee....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh.............eeeeeeee..eeeeeeeeehhhhhhhhhhhhhh..hhhhhh..eeee........eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sa3 B   1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
                                    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  


Chain C from PDB  Type:DNA  Length:9
                                         
                 1sa3 C   1 CCCCCGGGG   9


Chain D from PDB  Type:DNA  Length:9
                                         
                 1sa3 D  12 CCCCGGGGG  20


Chain E from PDB  Type:DNA  Length:9
                                         
                 1sa3 E   1 CCCCCGGGG   9


Chain F from PDB  Type:DNA  Length:9
                                         
                 1sa3 F  12 CCCCGGGGG  20
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SA3)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Endonuc-MspI] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T2M1_MORSP | P11405)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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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        T2M1_MORSP | P11405: 1yfi

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