1A79 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

Authors :   H. Li, C. R. Trotta, J. N. Abelson

Date :   23 Mar 98 (Deposition) - 01 Jun 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Endonuclease, Trna Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Li, C. R. Trotta, J. Abelson
Crystal Structure And Evolution Of A Transfer Rna Splicing Enzyme.
Science V. 280 279 1998
PubMed-ID: 9535656 | Reference-DOI: 10.1126/SCIENCE.280.5361.279
(for further references see the PDB file header)

Molecule 1 - TRNA ENDONUCLEASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Variant	:	BLR (DE3)
	Expression System Vector	:	PET11A
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	AU	4	Ligand/Ion	GOLD ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:108 , ARG A:113 , TYR A:115 , HIS A:125 , SER A:126 , LYS A:156	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	TYR C:108 , ARG C:113 , TYR C:115 , HIS C:125 , SER C:126 , LYS C:156	BINDING SITE FOR RESIDUE SO4 C 2
3	AC3	SOFTWARE	CYS D:86 , LEU D:87	BINDING SITE FOR RESIDUE AU D 1
4	AC4	SOFTWARE	CYS B:86 , LEU B:87	BINDING SITE FOR RESIDUE AU B 2
5	AC5	SOFTWARE	TYR C:75 , CYS C:86	BINDING SITE FOR RESIDUE AU C 3
6	AC6	SOFTWARE	TYR A:75 , CYS A:86	BINDING SITE FOR RESIDUE AU A 4

(no "SS Bond" information available for 1A79)

(no "Cis Peptide Bond" information available for 1A79)

(no "SAP(SNP)/Variant" information available for 1A79)

(no "PROSITE Motif" information available for 1A79)

(no "Exon" information available for 1A79)

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:171
 aligned with ENDA_METJA | Q58819 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:171
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 
           ENDA_METJA     9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
               SCOP domains d1a79a2 A:9-82 Tetrameric tRNA splicing endonuclease, N-terminal domain   d1a79a1 A:83-179 Tetrameric tRNA splicing endonuclease, C-terminal domain                         SCOP domains
               CATH domains 1a79A02 A:9-79  [code=3.40.1170.20, no name defined]                   1a79A01 A:80-179  [code=3.40.1350.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee..hhhhhhhhh..........eeeehhhhhhhhhh..eeee........hhhhhhhhhhh...hhhhhhhhhhhhh...eeee.hhh...eeee............eeeeeee......hhhhhhhhhhhhh...eeeeeee.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a79 A   9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with ENDA_METJA | Q58819 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:171
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 
           ENDA_METJA     9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
               SCOP domains d1a79b2 B:9-82 Tetrameric tRNA splicing endonuclease, N-terminal domain   d1a79b1 B:83-179 Tetrameric tRNA splicing endonuclease, C-terminal domain                         SCOP domains
               CATH domains 1a79B02 B:9-79  [code=3.40.1170.20, no name defined]                   1a79B01 B:80-179  [code=3.40.1350.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee..hhhhhhhhh..........eeeehhhhhhhhhh..eeee........hhhhhhhhhh....hhhhhhhhhhhhh...eeee.hhh...eeee............eeeeeee......hhhhhhhhhhhhhh..eeeeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a79 B   9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain C from PDB  Type:PROTEIN  Length:171
 aligned with ENDA_METJA | Q58819 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:171
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 
           ENDA_METJA     9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
               SCOP domains d1a79c2 C:9-82 Tetrameric tRNA splicing endonuclease, N-terminal domain   d1a79c1 C:83-179 Tetrameric tRNA splicing endonuclease, C-terminal domain                         SCOP domains
               CATH domains 1a79C02 C:9-79  [code=3.40.1170.20, no name defined]                   1a79C01 C:80-179  [code=3.40.1350.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee..hhhhhhhhh..........eeeehhhhhhhhh...eeee........hhhhhhhhhhh...hhhhhhhhhhhhh...eeee.hhh...eeee............eeeeeee......hhhhhhhhhhhhh...eeeeeee.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a79 C   9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain D from PDB  Type:PROTEIN  Length:171
 aligned with ENDA_METJA | Q58819 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:171
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 
           ENDA_METJA     9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
               SCOP domains d1a79d2 D:9-82 Tetrameric tRNA splicing endonuclease, N-terminal domain   d1a79d1 D:83-179 Tetrameric tRNA splicing endonuclease, C-terminal domain                         SCOP domains
               CATH domains 1a79D02 D:9-79  [code=3.40.1170.20, no name defined]                   1a79D01 D:80-179  [code=3.40.1350.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee..hhhhhhhhhh.........eeeehhhhhhhhhh..eeee........hhhhhhhhhh....hhhhhhhhhhhhh...eeee.hhh...eeee............eeeeeee......hhhhhhhhhhhhhh..eeeeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a79 D   9 KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP 179
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: MutS, DNA mismatch repair protein, domain I (15)

Homologous Superfamily: [code=3.40.1170.20, no name defined] (2)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

1a	1a79A02	A:9-79
1b	1a79B02	B:9-79
1c	1a79C02	C:9-79
1d	1a79D02	D:9-79

Topology: Trna Endonuclease; Chain: A, domain 1 (24)

Homologous Superfamily: [code=3.40.1350.10, no name defined] (24)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

2a	1a79A01	A:80-179
2b	1a79B01	B:80-179
2c	1a79C01	C:80-179
2d	1a79D01	D:80-179

(no "Pfam Domain" information available for 1A79)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (ENDA_METJA | Q58819)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000213	tRNA-intron endonuclease activity	Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
	GO:0000379	tRNA-type intron splice site recognition and cleavage	RNA processing that begins when the tertiary structure of a tRNA type intron is recognized, and ends when the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs.
cellular component
	GO:0000214	tRNA-intron endonuclease complex	A protein complex that catalyzes the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1a79)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 8)

CATH Domains (2, 8)

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Gene Ontology (11, 11)

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