3AJV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   SPLICING ENDONUCLEASE FROM AEROPYRUM PERNIX

Authors :   S. Yoshinari, Y. Watanabe, M. Okuda, T. Shiba, K. D. Inaoka, G. Kurisu

Date :   19 Jun 10 (Deposition) - 17 Nov 10 (Release) - 05 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Enda, Splicing Endonuclease, Trna Splicing, Archaea Crenarchaea, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Okuda, T. Shiba, D. K. Inaoka, K. Kita, G. Kurisu, S. Mineki, S. Harada, Y. Watanabe, S. Yoshinari
A Conserved Lysine Residue In The Crenarchaea-Specific Loop Is Important For The Crenarchaeal Splicing Endonuclease Activity.
J. Mol. Biol. V. 405 92 2011
PubMed-ID: 21050862 | Reference-DOI: 10.1016/J.JMB.2010.10.050

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET-6XHIS-APE-ENDA
	Expression System Strain	:	ROSETTA-GAMI(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PETDUET-1
	Gene	:	APE0685, APE1646, APE_0685
	Mutation	:	YES
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	272557
	Strain	:	K1
	Synonym	:	TRNA-SPLICING ENDONUCLEASE SUBUNIT ALPHA

Molecule 2 - TRNA-SPLICING ENDONUCLEASE
	Chains	:	B, D
	EC Number	:	3.1.27.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ENDA, APE_1646.1
	Mutation	:	YES
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	56636
	Synonym	:	TRNA-INTRON ENDONUCLEASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	10	Ligand/Ion	GLYCEROL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:82 , LEU A:83 , ASP A:84 , SER A:123 , TYR A:126 , HOH A:548 , ASP D:17 , HOH D:255	BINDING SITE FOR RESIDUE GOL A 171
02	AC2	SOFTWARE	ASP A:91 , LYS A:95 , ILE A:158 , TYR A:160 , HOH A:187 , HOH B:484	BINDING SITE FOR RESIDUE GOL A 172
03	AC3	SOFTWARE	ARG B:126 , ALA B:134 , PRO B:135 , PHE B:136 , ARG B:163 , HOH B:212 , HOH B:383	BINDING SITE FOR RESIDUE GOL B 187
04	AC4	SOFTWARE	ARG B:154 , HOH B:231 , HOH B:413 , HOH B:481 , HOH B:544 , GLY D:119 , ASP D:121 , HOH D:252	BINDING SITE FOR RESIDUE GOL B 188
05	AC5	SOFTWARE	TYR B:31 , GLU B:43 , LYS B:44 , ARG B:113 , PRO B:129 , HOH B:354 , HOH B:545	BINDING SITE FOR RESIDUE GOL B 189
06	AC6	SOFTWARE	PRO B:39 , LEU B:40 , HOH B:401 , ARG C:94 , GLY C:156 , LEU C:157 , ILE C:158	BINDING SITE FOR RESIDUE GOL B 190
07	AC7	SOFTWARE	SER B:57 , ILE B:59 , HOH B:289 , ARG C:154 , HOH C:190	BINDING SITE FOR RESIDUE CL B 191
08	AC8	SOFTWARE	ASP B:17 , HOH B:248 , SER C:82 , LEU C:83 , ASP C:84 , SER C:123 , HOH C:211	BINDING SITE FOR RESIDUE GOL C 171
09	AC9	SOFTWARE	ALA D:134 , PRO D:135 , ARG D:163 , HOH D:194 , HOH D:360	BINDING SITE FOR RESIDUE GOL D 187
10	BC1	SOFTWARE	ARG B:94 , ASP B:121 , HOH B:353 , VAL D:150 , GLU D:151 , ARG D:154 , HOH D:217 , HOH D:452	BINDING SITE FOR RESIDUE GOL D 188
11	BC2	SOFTWARE	TYR D:31 , TYR D:35 , PRO D:45 , PRO D:129 , GLY D:130	BINDING SITE FOR RESIDUE GOL D 189
12	BC3	SOFTWARE	ARG A:154 , HOH A:198 , SER D:57 , ILE D:59	BINDING SITE FOR RESIDUE CL D 190

Asymmetric/Biological Unit

No.	Residues
1	A:11	-	A:62
2	A:27	-	A:33
3	C:11	-	C:62
4	C:27	-	C:33

Asymmetric/Biological Unit

No.	Residues
1	Gly B:52	-	Pro B:53
2	Gly D:52	-	Pro D:53

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

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

(no "Exon" information available for 3AJV)

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:168
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        
         Q9YE85_AERPE     3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee.hhhhhhhhhhh..ee..eehhhhhhhhhhh..eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhh....ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ajv A   3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
           ENDA_AERPE     7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeee.hhhhhhhhhhh....ee..............eeeehhhhhhhhhh..eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeee....ee.hhhhhhhhhhhh....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ajv B   7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDAAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q9YE85_AERPE    10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee.hhhhhhhhhhh..ee..eehhhhhhhhhhh..eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ajv C  10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169

Chain D from PDB  Type:PROTEIN  Length:178
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:178
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178        
           ENDA_AERPE     9 KASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee.hhhhhhhhhhh....ee..............eeeehhhhhhhhhh..eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeee....ee.hhhhhhhhhhhh....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ajv D   9 KASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDAAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    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 '\|'

(no "SCOP Domain" information available for 3AJV)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (Q9YE85_AERPE | Q9YE85)

molecular function
	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: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.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (ENDA_AERPE | Q9YBF1)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly B:52 - Pro B:53	[ RasMol ]
		Gly D:52 - Pro D:53	[ RasMol ]

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	3ajv
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	Q9YE85_AERPE \| Q9YE85
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	3.1.27.9
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	ENDA_AERPE \| Q9YBF1	:	3p1y 3p1z
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	Q9YE85_AERPE \| Q9YE85	:	3p1z

(no "Related Entries Specified in the PDB File" available for 3AJV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (11, 18)

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