3NGY - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RNASE T (E92G MUTANT)

Authors :   Y. -Y. Hsiao, H. S. Yuan

Date :   14 Jun 10 (Deposition) - 16 Feb 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E  (1x)

Keywords :   Exoribonuclease, Rna Processing, Rna Maturation, Protein-Dna Interactions, Exo-Nuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -Y. Hsiao, C. -C. Yang, C. L. Lin, J. L. J. Lin, Y. Duh, H. S. Yuan
Structural Basis For Rna Trimming By Rnase T In Stable Rna 3'-End Maturation
Nat. Chem. Biol. V. 7 236 2011
PubMed-ID: 21317904 | Reference-DOI: 10.1038/NCHEMBIO.524

Molecule 1 - RIBONUCLEASE T
	Chains	:	A, B, C, D
	EC Number	:	3.1.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNT
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	JM109 / ATCC 53323
	Synonym	:	RNASE T, EXORIBONUCLEASE T

Molecule 2 - HIS TAG SEQUENCE
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	RIPL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNT
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	JM109 / ATCC 53323

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CO	3	Ligand/Ion	COBALT (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:135 , HOH A:224 , HOH A:226	BINDING SITE FOR RESIDUE CO A 216
2	AC2	SOFTWARE	ARG B:135	BINDING SITE FOR RESIDUE CO B 216
3	AC3	SOFTWARE	ARG D:135	BINDING SITE FOR RESIDUE CO D 216

Asymmetric Unit

No.	Residues
1	A:11	-	A:112
2	B:11	-	B:112
3	C:11	-	C:112
4	D:11	-	D:112

Asymmetric Unit

No.	Residues
1	Trp A:207	-	Pro A:208
2	Trp B:207	-	Pro B:208
3	Trp C:207	-	Pro C:208
4	Leu C:209	-	Ser C:210
5	Trp D:207	-	Pro D:208

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

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

(no "Exon" information available for 3NGY)

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:204
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:204
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
            RNT_ECOLI     9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
               SCOP domains d3ngya_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngy A   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSAA 212
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:202
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
            RNT_ECOLI     8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
               SCOP domains d3ngyb_ B: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngy B   8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:202
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
            RNT_ECOLI     9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLS 210
               SCOP domains d3ngyc_ C: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeee....--------------------..eehhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngy C   9 GLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVG--------------------GAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLS 210
                                    18        28        38        48        58        |-         -        88        98       108       118       128       138       148       158       168       178       188       198       208  
                                                                                     67                   88

Chain D from PDB  Type:PROTEIN  Length:202
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:202
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  
            RNT_ECOLI     8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
               SCOP domains d3ngyd_ D: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------RNase_T-3ngyD01 D:20-194                                                                                                                                                       --------------- Pfam domains (1)
           Pfam domains (2) ------------RNase_T-3ngyD02 D:20-194                                                                                                                                                       --------------- Pfam domains (2)
           Pfam domains (3) ------------RNase_T-3ngyD03 D:20-194                                                                                                                                                       --------------- Pfam domains (3)
           Pfam domains (4) ------------RNase_T-3ngyD04 D:20-194                                                                                                                                                       --------------- Pfam domains (4)
         Sec.struct. author .hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngy D   8 TGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3ngy E   1 SHHHHH   6

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: DnaQ-like 3'-5' exonuclease (253)

Protein domain: automated matches (19)

Escherichia coli [TaxId: 562] (13)

1a	d3ngya_	A:
1b	d3ngyb_	B:
1c	d3ngyc_	C:
1d	d3ngyd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: RNase_T (14)

Escherichia coli (strain K12) (6)

1a	RNase_T-3ngyD01	D:20-194
1b	RNase_T-3ngyD02	D:20-194
1c	RNase_T-3ngyD03	D:20-194
1d	RNase_T-3ngyD04	D:20-194

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RNT_ECOLI | P30014)

molecular function
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016896	exoribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu C:209 - Ser C:210	[ RasMol ]
		Trp A:207 - Pro A:208	[ RasMol ]
		Trp B:207 - Pro B:208	[ RasMol ]
		Trp C:207 - Pro C:208	[ RasMol ]
		Trp D:207 - Pro D:208	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	3ngy
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	RNT_ECOLI \| P30014
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	3.1.13.-
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	RNT_ECOLI \| P30014
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UniProtKB/Swiss-Prot
	RNT_ECOLI \| P30014	:	2is3 3ngz 3nh0 3nh1 3nh2 3v9s 3v9u 3v9w 3v9x 3v9z 3va0 3va3 4kaz 4kb0 4kb1

3ngz	RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA (GC) WITH ONE MG IN THE ACTIVE SITE
3nh0	RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA (AAC)
3nh1	RNASE T IN COMPLEX WITH A PREFERRED SSDNA (TAGG) WITH TWO MG IN THE ACTIVE SITE
3nh2	RNASE T IN COMPLEX WITH A STEM DNA WITH A 3' OVERHANG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Gene Ontology (14, 14)

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Related Entries Specified in the PDB File