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(-) Description

Title :  EXPANDING LAGALIDADG ENDONUCLEASE SCAFFOLD DIVERSITY BY RAPIDLY SURVEYING EVOLUTIONARY SEQUENCE SPACE
 
Authors :  K. Jacoby, M. Metzger, B. Shen, J. Jarjour, B. Stoddard, A. Scharenberg
Date :  29 Nov 11  (Deposition) - 29 Feb 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Laglidagd Endonuclease, Hydrolase, Divalent Metal Ions, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Jacoby, M. Metzger, B. W. Shen, M. T. Certo, J. Jarjour, B. L. Stoddard, A. M. Scharenberg
Expanding Laglidadg Endonuclease Scaffold Diversity By Rapidly Surveying Evolutionary Sequence Space.
Nucleic Acids Res. V. 40 4954 2012
PubMed-ID: 22334611  |  Reference-DOI: 10.1093/NAR/GKR1303

(-) Compounds

Molecule 1 - INTRON-ENCODED DNA ENDONUCLEASE I-HJEMI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B(+)
    Expression System Strain: RIL+
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: I-HJEMI
    Gene: I-ANII
    Mutation: YES
    Organism Scientific: TRICHODERMA REESEI
    Organism Taxid: 51453
    Synonym: COB INTRON PROTEIN, MRNA MATURASE BI1, TRUNCATED NON- FUNCTIONAL CYTOCHROME B, DNA ENDONUCLEASE/RNA MATURASE I-ANII
 
Molecule 2 - SYNTHETIC OLIGO
    Chains: C, E
    Engineered: YES
    Other Details: SYNTHETIC OLIGO
    Synthetic: YES
 
Molecule 3 - SYNTHETIC OLIGO
    Chains: D, F
    Engineered: YES
    Other Details: SYNTHETIC OLIGO
    Synthetic: YES

 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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:18 , ALA A:149 , HOH A:416 , DT C:417 , DA D:515BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREGLU A:16 , GLY A:17 , GLU A:150 , CA A:303 , HOH A:415 , DC C:416 , DC D:516BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREGLY A:17 , ASP A:18 , GLU A:150 , CA A:302 , DC C:416 , DT C:417 , DA D:515 , DC D:516BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP B:18 , ALA B:149 , DT E:417 , DA F:514 , DA F:515BINDING SITE FOR RESIDUE CA B 301
05AC5SOFTWARELYS B:76 , ASN B:77 , LYS B:80 , HOH B:441BINDING SITE FOR RESIDUE PEG B 302
06AC6SOFTWAREASP B:75 , ASN B:77BINDING SITE FOR RESIDUE NA B 304
07AC7SOFTWAREGLU B:150 , DT E:415 , DC E:416 , DC F:516BINDING SITE FOR RESIDUE CA E 501
08AC8SOFTWAREDG E:409 , PEG E:503BINDING SITE FOR RESIDUE CA E 502
09AC9SOFTWAREDG E:409 , CA E:502 , HOH E:625BINDING SITE FOR RESIDUE PEG E 503
10BC1SOFTWAREDC F:525 , HOH F:719 , HOH F:726BINDING SITE FOR RESIDUE PEG F 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UVF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:158 -Asn A:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UVF)

(-) Exons   (0, 0)

(no "Exon" information available for 3UVF)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhheeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...................hhhhhhh..hhhhhhhhhhhhhheeeeee.......eeeeeeeeee.hhhhhhhhhhhh......ee....eeeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uvf A   2 SHMDLTYAYLVGLFEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKDILGVGKVSFRKRNEIEMVSLRIRDKNHLKNFILPIFDKYPMLSNKQYDYLRFKDALLSNIIYSDDLPEYARSNESINSVDSIINTSYFSAWLVGFIEAEGCFSTYKLNKDDDYLIASFDIAQKDGDILISAIHKYLSFTTKIYLDKTNCSRLKVTGVRSVKNVVKFIQGAPVKLLGNKKLQYKLWIKQLRKISRYSEKIQLPSNY 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhheeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhh...eeeee....eeeeee..hhhhhhhh............hhhhhhhhhhhhhhhh..................hhhhhhh..hhhhhhhhhhhhhh.eeeee.......eeeeeeeeee.hhhhhhhhhhhh......ee....eeeeeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uvf B   2 SHMDLTYAYLVGLFEGDGYFSITKKGKYLTYELGIELSIKDVQLIYKIKDILGVGKVSFRKRNEIEMVSLRIRDKNHLKNFILPIFDKYPMLSNKQYDYLRFKDALLSNIIYSDDLPEYARSNESINSVDSIINTSYFSAWLVGFIEAEGCFSTYKLNKDDDYLIASFDIAQKDGDILISAIHKYLSFTTKIYLDKTNCSRLKVTGVRSVKNVVKFIQGAPVKLLGNKKLQYKLWIKQLRKISRYSEKIQLPSNY 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     


Chain C from PDB  Type:DNA  Length:28
                                                            
                 3uvf C 401 GCGCTGAGGAGGTTTCTCTGTTAAGCGA 428
                                   410       420        


Chain D from PDB  Type:DNA  Length:28
                                                            
                 3uvf D 501 CGCTTAACAGAGAAACCTCCTCAGCGCT 528
                                   510       520        


Chain E from PDB  Type:DNA  Length:28
                                                            
                 3uvf E 401 GCGCTGAGGAGGTTTCTCTGTTAAGCGA 428
                                   410       420        


Chain F from PDB  Type:DNA  Length:28
                                                            
                 3uvf F 501 CGCTTAACAGAGAAACCTCCTCAGCGCT 528
                                   510       520
   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 3UVF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UVF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UVF)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3UVF)

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(-) Related Entries Specified in the PDB File

1p8k THE STRUCTURE AND DNA RECOGNITION OF A BIFUNCTIONAL HOMING ENDONUCLEASE AND GROUP I INTRON SPLICING FACTOR
2qoj COEVOLUTION OF A HOMING ENDONUCLEASE AND ITS HOST TARGET SEQUENCE
3ehb CRYSTAL STRUCTURE OF Y2 I-ANII VARIANT (F13Y/S111Y)/DNA COMPLEX WITH CALCIUM