3C0X - JenaLib

Title :   I-SCEI IN COMPLEX WITH A TOP NICKED DNA SUBSTRATE

Authors :   C. M. Moure, F. S. Gimble, F. A. Quiocho

Date :   21 Jan 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Endonuclease, Homing, Ladlidadg, Catalytic Mechanism, Metal Binding, Nicked Intermediate, Hydrolase, Intron Homing, Mitochondrion, Mrna Processing, Mrna Splicing, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Moure, F. S. Gimble, F. A. Quiocho
Crystal Structures Of I-Scei Complexed To Nicked Dna Substrates: Snapshots Of Intermediates Along The Dna Cleavage Reaction Pathway.
Nucleic Acids Res. V. 36 3287 2008
PubMed-ID: 18424798 | Reference-DOI: 10.1093/NAR/GKN178
(for further references see the PDB file header)

Compounds

Molecule 1 - INTRON-ENCODED ENDONUCLEASE I-SCEI
	Chains	:	A
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET15
	Gene	:	SCEI, OMEGA, SECY
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA

*Molecule 2 - DNA (5'- D(DCDAPDCPDGPDCPDTPDAPDGPDGPDGPDAPDTPDAPDA)- 3')*
	Chains	:	B
	Engineered	:	YES
	Other Details	:	DNA TOP STRAND B
	Other Details - Source	:	DNA SYNTHETIC PRODUCT
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(PDCPDAPDGPDGPDGPDTPDAPDAPDTPDAPDC)-3')**
	Chains	:	C
	Engineered	:	YES
	Other Details	:	DNA TOP STRAND C
	Other Details - Source	:	DNA SYNTHETIC PRODUCT
	Synthetic	:	YES

*Molecule 4 - DNA (5'- D(DGDGPDTPDAPDTPDTPDAPDCPDCPDCPDTPDGPDTPDTPD APDTPDCPDCPDCPDTPDAPDGPDCPDGPDT)-3')**
	Chains	:	D
	Engineered	:	YES
	Other Details	:	DNA BOTTOM STRAND D
	Other Details - Source	:	DNA SYNTHETIC PRODUCT
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 1)

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:223
 aligned with SCE1_YEAST | P03882 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           SCE1_YEAST     3 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLP 225
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c0xA01 A:3-122 Homing endonucleases                                                                                    3c0xA02 A:123-225 Homing endonucleases                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee...hhhhhhhhh..ee..ee....hhhhhhhhhhhhhhhhhhheee...........eee.....hhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-225 UniProt: 1-235 [INCOMPLETE]                                                                                                                                                                              Transcript 1
                 3c0x A   3 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLP 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:DNA  Length:13
                                             
                 3c0x B   2 ACGCTAGGGATAA  14
                                    11

Chain C from PDB  Type:DNA  Length:11
                                           
                 3c0x C  15 CAGGGTAATAC  25
                                    24

Chain D from PDB  Type:DNA  Length:24
                                                        
                 3c0x D   2 GTATTACCCTGTTATCCCTAGCGT  25
                                    11        21

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SCE1_YEAST | P03882)

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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006314	intron homing	Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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