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(-) Description

Title :  CRYSTAL STRUCTURE OF SPECIFIC RESTRICTION ENDONUCLEASE AGEI-DNA COMPLEX
 
Authors :  G. Tamulaitiene, V. Jovaisaite, S. Grazulis, V. Siksnys
Date :  22 Sep 15  (Deposition) - 28 Sep 16  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Endonuclease, Pd-(D/E)Xk Nuclease, Protein-Dna Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Tamulaitiene, V. Jovaisaite, G. Tamulaitis, I. Songailiene, E. Manakova, M. Zaremba, S. Grazulis, S. Y. Xu, V. Siksnys
Restriction Endonuclease Agei Is A Monomer Which Dimerizes To Cleave Dna.
Nucleic Acids Res. V. 45 3547 2017
PubMed-ID: 28039325  |  Reference-DOI: 10.1093/NAR/GKW1310

(-) Compounds

Molecule 1 - TYPE-2 RESTRICTION ENZYME AGEI
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRRS-AGEIRM
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AGEIR
    Organism Scientific: THALASSOBIUS GELATINOVORUS
    Organism Taxid: 53501
    Synonym: R.AGEI,ENDONUCLEASE AGEI,TYPE II RESTRICTION ENZYME AGEI
 
Molecule 2 - DNA (5'-D(*TP*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*GP*A*)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5DWB)

(-) Sites  (0, 0)

(no "Site" information available for 5DWB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DWB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:204 -Pro A:205
2Pro B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DWB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DWB)

(-) Exons   (0, 0)

(no "Exon" information available for 5DWB)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...........eeeeee..........eeeeeeeeee....hhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhh.....eeee.................eee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwb A   1 MRLDLDFGRGLVAHVMLDNVSEEQYQQISDYFVPLVNKPKLKSRDAIGQAFVMATEVCPDANPSDLWHHVLYRIYIREKIGTDPSQSWVRTSGEAFEVALVERYNPVLARHGIRLTALFKGQKGLALTRMGVADRVGSRKVDVMIEKQGGGRSPDAEGFGVVGGIHAKVSLAERVSDDIPASRIMMGEGLLSVLSTLDVKSFPPPHGDLVNRGELGTPDRPSDKRNYIEGHGDFSACFSYNLRTSPSNATTPSGRHIYVSGFSGQDDEFTDYLVAQLA 278
                                    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        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...........eeeeee..........eeeeeeeeee....hhhhhhhhhhhhhhh...eeeeee.........................hhhhhhhhh.....eeee.................eee.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwb B   1 MRLDLDFGRGLVAHVMLDNVSEEQYQQISDYFVPLVNKPKLKSRDAIGQAFVMATEVCPDANPSDLWHHVLYRIYIREKIGTDPSQSWVRTSGEAFEVALVERYNPVLARHGIRLTALFKGQKGLALTRMGVADRVGSRKVDVMIEKQGGGRSPDAEGFGVVGGIHAKVSLAERVSDDIPASRIMMGEGLLSVLSTLDVKSFPPPHGDLVNRGELGTPDRPSDKRNYIEGHGDFSACFSYNLRTSPSNATTPSGRHIYVSGFSGQDDEFTDYLVAQLA 278
                                    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        


Chain C from PDB  Type:DNA  Length:13
                                             
                 5dwb C  -3 TTCGACCGGTCGA   9
                                     6   


Chain D from PDB  Type:DNA  Length:13
                                             
                 5dwb D  -3 TTCGACCGGTCGA   9
                                     6
   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 5DWB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DWB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DWB)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro A:204 - Pro A:205   [ RasMol ]  
    Pro B:204 - Pro B:205   [ RasMol ]  
 

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        T2A1_THAGE | Q9KHV6: 5dwa 5dwc

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