2IS3 - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE T

Authors :   Y. Zuo, Y. Wang, A. Malhotra

Date :   16 Oct 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (8x)
Biol. Unit 4: A,B,C,D  (4x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6: A,B,C,D  (1x)

Keywords :   Rnase, Ribonuclease, Exoribonuclease, Exonuclease, Nuclease, Hydrolase, Stable Rna Maturation, Trna End-Turnover (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zuo, H. Zheng, Y. Wang, M. Chruszcz, M. Cymborowski, T. Skarina, A. Savchenko, A. Malhotra, W. Minor
Crystal Structure Of Rnase T, An Exoribonuclease Involved I Trna Maturation And End Turnover.
Structure V. 15 417 2007
PubMed-ID: 17437714 | Reference-DOI: 10.1016/J.STR.2007.02.004

Molecule 1 - RIBONUCLEASE T
	Chains	:	A, B, C, D
	EC Number	:	3.1.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PUC19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RNT
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	EXORIBONUCLEASE T, RNASE T

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (8x)	:	A	B	C	D
Biological Unit 4 (4x)	:	A	B	C	D
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 6 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 37)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	13	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 19)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 296)

No.	Name	Count	Type	Full Name
1	MSE	192	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	104	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 148)

No.	Name	Count	Type	Full Name
1	MSE	96	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	52	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 19)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 37)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	13	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:15 , HIS A:144 , MSE C:173 , ASP C:174 , ARG C:189	BINDING SITE FOR RESIDUE SO4 C 216
02	AC2	SOFTWARE	SER A:137 , LEU A:138 , LYS A:139 , ARG A:140	BINDING SITE FOR RESIDUE SO4 A 216
03	AC3	SOFTWARE	MSE B:173 , ASP B:174 , ARG B:189	BINDING SITE FOR RESIDUE SO4 B 216
04	AC4	SOFTWARE	LYS B:101 , ARG B:104 , ARG B:140	BINDING SITE FOR RESIDUE SO4 B 217
05	AC5	SOFTWARE	HIS B:97 , ARG B:104 , LEU B:138 , LYS B:139 , ARG B:140	BINDING SITE FOR RESIDUE SO4 B 218
06	AC6	SOFTWARE	ARG C:104 , LEU C:138 , LYS C:139 , ARG C:140	BINDING SITE FOR RESIDUE SO4 C 217
07	AC7	SOFTWARE	LEU D:10 , LYS D:45 , MSE D:46 , SER D:110	BINDING SITE FOR RESIDUE SO4 D 216
08	AC8	SOFTWARE	ARG D:15 , HIS D:144	BINDING SITE FOR RESIDUE SO4 D 217
09	AC9	SOFTWARE	MSE D:173 , ASP D:174 , ARG D:189	BINDING SITE FOR RESIDUE SO4 D 218
10	BC1	SOFTWARE	MSE A:173 , ASP A:174 , ARG A:189	BINDING SITE FOR RESIDUE SO4 A 217
11	BC2	SOFTWARE	GLY A:9 , LEU A:10 , MSE A:46 , SER A:110	BINDING SITE FOR RESIDUE SO4 A 218
12	BC3	SOFTWARE	GLY B:9 , LEU B:10 , LYS B:45 , MSE B:46 , SER B:110	BINDING SITE FOR RESIDUE SO4 B 219
13	BC4	SOFTWARE	LEU C:10 , MSE C:46	BINDING SITE FOR RESIDUE SO4 C 218

(no "SS Bond" information available for 2IS3)

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	Trp D:207	-	Pro D:208

(no "SAP(SNP)/Variant" information available for 2IS3)

(no "PROSITE Motif" information available for 2IS3)

(no "Exon" information available for 2IS3)

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:203
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
            RNT_ECOLI     7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
               SCOP domains d2is3a_ A: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 2is3A00 A:7-209  [code=3.30.420.10, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2is3 A   7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKmDEQGWLmPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAImVAHNANFDHSFmmAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGmDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
                                    16        26        36        46      | 56        66        76        86        96       106       116|      126  ||   136       146       156       166      |176       186       196       206   
                                                                  46-MSE 53-MSE                                                         117-MSE     129-MSE                                     173-MSE                                
                                                                                                                                                     130-MSE

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:205
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206     
            RNT_ECOLI     7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSA 211
               SCOP domains d2is3b_ B: automated           matches                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeeee.----------.eeeeeeeee.....eeeeeeeeeeee.-----------------------..eehhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2is3 B   7 LTGLCDRFRGFYPVVIDVET----------LEIAAITLKmDEQGWLmPDTTLHFHVEP-----------------------GAVSEYEALHEIFKVVRKGIKASGCNRAImVAHNANFDHSFmmAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGmDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPLSA 211
                                    16        26         -|       46      | 56       | -         -         - |      96       106       116|      126  ||   136       146       156       166      |176       186       196       206     
                                              26         37       46-MSE 53-MSE     64                      88                          117-MSE     129-MSE                                     173-MSE                                  
                                                                                                                                                     130-MSE

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
            RNT_ECOLI     7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
               SCOP domains d2is3c_ C: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 2is3C00 C:7-209  [code=3.30.420.10, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeee.........hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhh..hhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2is3 C   7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKmDEQGWLmPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAImVAHNANFDHSFmmAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGmDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
                                    16        26        36        46      | 56        66        76        86        96       106       116|      126  ||   136       146       156       166      |176       186       196       206   
                                                                  46-MSE 53-MSE                                                         117-MSE     129-MSE                                     173-MSE                                
                                                                                                                                                     130-MSE

Chain D from PDB  Type:PROTEIN  Length:203
 aligned with RNT_ECOLI | P30014 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
            RNT_ECOLI     7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
               SCOP domains d2is3d_ D: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 2is3D00 D:7-209  [code=3.30.420.10, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeee.......hhhhhhhhh..........eehhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2is3 D   7 LTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKmDEQGWLmPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAImVAHNANFDHSFmmAAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGmDFDSTQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209
                                    16        26        36        46      | 56        66        76        86        96       106       116|      126  ||   136       146       156       166      |176       186       196       206   
                                                                  46-MSE 53-MSE                                                         117-MSE     129-MSE                                     173-MSE                                
                                                                                                                                                     130-MSE

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 K-12 [TaxId: 83333] (2)

1a	d2is3a_	A:
1b	d2is3b_	B:
1c	d2is3c_	C:
1d	d2is3d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. (1)

1a	2is3A00	A:7-209
1b	2is3C00	C:7-209
1c	2is3D00	D:7-209

(no "Pfam Domain" information available for 2IS3)

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.

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	Cis Peptide Bonds
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		Trp B:207 - Pro B:208	[ RasMol ]
		Trp C:207 - Pro C:208	[ RasMol ]
		Trp D:207 - Pro D:208	[ RasMol ]

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	RNT_ECOLI \| P30014	:	3ngy 3ngz 3nh0 3nh1 3nh2 3v9s 3v9u 3v9w 3v9x 3v9z 3va0 3va3 4kaz 4kb0 4kb1

2f96	ORTHOLOGOUS PROTEIN FROM A DIFFERENT ORGANISM AND DESCRIBED IN THE SAME PUBLICATION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 37)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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