1WDU - JenaLib

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Title :   ENDONUCLEASE DOMAIN OF TRAS1, A TELOMERE-SPECIFIC NON-LTR RETROTRANSPOSON

Authors :   N. Maita, T. Anzai, H. Aoyagi, H. Mizuno, H. Fujiwara

Date :   17 May 04 (Deposition) - 10 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Four-Layered Alpha/Beta Sandwich, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Maita, T. Anzai, H. Aoyagi, H. Mizuno, H. Fujiwara
Crystal Structure Of The Endonuclease Domain Encoded By The Telomere-Specific Long Interspersed Nuclear Element, Tras1
J. Biol. Chem. V. 279 41067 2004
PubMed-ID: 15247245 | Reference-DOI: 10.1074/JBC.M406556200
(for further references see the PDB file header)

Molecule 1 - TRAS1 ORF2P
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Mutation	:	YES
	Organism Common	:	DOMESTIC SILKWORM
	Organism Scientific	:	BOMBYX MORI
	Organism Taxid	:	7091

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:29 , GLN A:31 , GLU A:56 , TYR A:126 , ASP A:157 , ASN A:159 , HIS A:237 , HOH A:260	BINDING SITE FOR RESIDUE PO4 A 249
2	AC2	SOFTWARE	LYS B:168 , SER B:208 , ARG B:209	BINDING SITE FOR RESIDUE CL B 249
3	AC3	SOFTWARE	SER A:167 , LYS A:168 , SER A:208 , ARG A:209	BINDING SITE FOR RESIDUE CL A 250

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

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

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

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

(no "Exon" information available for 1WDU)

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
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Chain A from PDB  Type:PROTEIN  Length:217
 aligned with Q93139_BOMMO | Q93139 from UniProtKB/TrEMBL  Length:1162

    Alignment length:223
                                                                   1                                                                                                                                                                                       
                                     -         -         -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
         Q93139_BOMMO     - ---------------------------------------MKGFRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLVSYYFEPDKPIESYLEQIKRVERKMGPKRLIFGGDANAKSTWWGCKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGGKRYQSRVDVTFCTEDMLDLIDGWRVDEDLVSSDHNGMVFNIRLQK 184
               SCOP domains d1wdua_ A: Endonuclease domain of TRAS1  retrotransposon (ORF2)                                                                                                                                                                 SCOP domains
               CATH domains 1wduA00 A:21-248  [code=3.60.10.10, no  name defined]                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhh..eeeee....-......eeee..........eeeee.....eeee........eeeeeee....eeeeeeee......hhhhhhhhhhhhhh.....eeeeee....hhhhh....hhhhhhhhhhhhhhh.ee........ee.-----..ee..eeeee.hhhh..eeeeee...........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wdu A  21 PPYRVLQANLQRKKLATAELAIEAATRKAAIALIQEPYV-KGFRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLVSYYFEPDKPIESYLEQIKRVERKMGPKRLIFGGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVPTFDT-----RYQSRVDVTFCTEDMLDLIDGWRVDEDLVSSDHNGMVFNIRLQK 248
                                    30        40        50        |-|       75        85        95       105       115       125       135       145       155       165       175       185       195   |   205       215       225       235       245   
                                                                 59 |                                                                                                                                  199   205                                           
                                                                   66

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with Q93139_BOMMO | Q93139 from UniProtKB/TrEMBL  Length:1162

    Alignment length:219
                                1 3                               4                                                                                                                                                                                    
                                | |  -         -         -        |5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175         
         Q93139_BOMMO     - ----MKG-------------------------------FRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLVSYYFEPDKPIESYLEQIKRVERKMGPKRLIFGGDANAKSTWWGCKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGGKRYQSRVDVTFCTEDMLDLIDGWRVDEDLVSSDHNGMVFNIRLQK 184
               SCOP domains d1wdub_ B: Endonuclease domain of TRAS1 retrotransposon (ORF2)                                                                                                                                                              SCOP domains
               CATH domains 1wduB00 B:22-248  [code=3.60.10.10, no name defined]                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhh..eeeee........eeee..........eeeee.....eeee........eeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhh...eeeeee....hhhhh....hhhhhhhhhhhhhhheee........eeeee..eeeee..eeeeee.hhhh.eeeeee...........eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wdu B  22 PYRVLQANLQRKKLATAELAIEAATRKAAIALIQEPYVFRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTTNNIVVVGIRTRAWEITLVSYYFEPDKPIESYLEQIKRVERKMGPKRLIFGGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGGKRYQSRVDVTFCTEDMLDLIDGWRVDEDLVSSDHNGMVFNIRLQK 248
                                    31        41        51       |69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
                                                                59|                                                                                                                                                                                    
                                                                 68

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	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 Unit

Classes(

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: DNase I-like (31)

Protein domain: Endonuclease domain of TRAS1 retrotransposon (ORF2) (1)

Silkworm (Bombyx mori) [TaxId: 7091] (1)

1a	d1wdua_	A:
1b	d1wdub_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Deoxyribonuclease I; Chain A (35)

Homologous Superfamily: [code=3.60.10.10, no name defined] (35)

Domestic silkworm (Bombyx mori) (1)

1a	1wduB00	B:22-248
1b	1wduA00	A:21-248

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q93139_BOMMO | Q93139)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	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.

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