3BK1 - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF RNASE J

Authors :   I. L. De La Sierra-Gallay, L. Zig, H. Putzer

Date :   05 Dec 07 (Deposition) - 22 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

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

Keywords :   Rnase J, Endoribonuclease, 5'-3' Exoribonuclease, Metal Dependent Hydrolase, Metallo-Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. L. De La Sierra-Gallay, L. Zig, A. Jamalli, H. Putzer
Structural Insights Into The Dual Activity Of Rnase J
Nat. Struct. Mol. Biol. V. 15 206 2008
PubMed-ID: 18204464 | Reference-DOI: 10.1038/NSMB.1376

Molecule 1 - METAL DEPENDENT HYDROLASE
	Chains	:	A
	EC Number	:	3.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 20-573
	Gene	:	TTC0775
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Strain	:	HB27
	Synonym	:	RNASE J

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 21)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 38)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	6	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:340 , HIS A:372 , SER A:374 , GLY A:375 , HIS A:376 , HOH A:952 , HOH A:994	BINDING SITE FOR RESIDUE SO4 A 945
2	AC2	SOFTWARE	GLN A:311 , PRO A:312 , MSE A:313 , PRO A:341 , ILE A:342 , ASN A:345 , VAL A:349 , HOH A:1113	BINDING SITE FOR RESIDUE SO4 A 946
3	AC3	SOFTWARE	ARG A:147 , HIS A:186 , ARG A:416 , HOH A:1027 , HOH A:1102 , HOH A:1122	BINDING SITE FOR RESIDUE SO4 A 947
4	AC4	SOFTWARE	HIS A:75 , HIS A:77 , HIS A:150 , ASP A:172 , ZN A:949 , HOH A:953	BINDING SITE FOR RESIDUE ZN A 948
5	AC5	SOFTWARE	ASP A:79 , HIS A:80 , ASP A:172 , HIS A:398 , ZN A:948 , HOH A:953	BINDING SITE FOR RESIDUE ZN A 949
6	AC6	SOFTWARE	GLN A:379 , ASN A:406	BINDING SITE FOR RESIDUE GOL A 601
7	AC7	SOFTWARE	THR A:178 , MSE A:218 , LYS A:222	BINDING SITE FOR RESIDUE GOL A 602

(no "SS Bond" information available for 3BK1)

Asymmetric Unit

No.	Residues
1	Pro A:366	-	Pro A:367

(no "SAP(SNP)/Variant" information available for 3BK1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUGAR_TRANSPORT_1	PS00216	Sugar transport proteins signature 1.	RNJ_THET2	268-285	1	A:250-267

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUGAR_TRANSPORT_1	PS00216	Sugar transport proteins signature 1.	RNJ_THET2	268-285	2	A:250-267

(no "Exon" information available for 3BK1)

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:551
 aligned with RNJ_THET2 | Q72JJ7 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:551
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572 
            RNJ_THET2    23 GPQDHVEIIPLGGMGEIGKNITVFRFRDEIFVLDGGLAFPEEGMPGVDLLIPRVDYLIEHRHKIKAWVLTHGHEDHIGGLPFLLPMIFGKESPVPIYGARLTLGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRMTHSIPDNSGVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADATNAERPGYTPSEMEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRKVAMEGRSMLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILATGSQGQPMSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQMNFKWLAESMSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVGDITEEILADRRHMAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVRRMALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPMILPVVIEG 573
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh......eeeee.....eeee...eeeeeee........eeeeeee..eeeee.................hhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..........hhhhhh..hhh.eeeee......hhhhhhhhhh............eeee.......hhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeee....eeeeee....eeeee..ee...hhhhhhhhhhhhhhheeeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUGAR_TRANSPORT_1 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bk1 A   5 GPQDHVEIIPLGGmGEIGKNITVFRFRDEIFVLDGGLAFPEEGmPGVDLLIPRVDYLIEHRHKIKAWVLTHGHEDHIGGLPFLLPmIFGKESPVPIYGARLTLGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRmTHSIPDNSGVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADATNAERPGYTPSEmEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRKVAmEGRSmLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILATGSQGQPmSVLHRLAFEGHAKmAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQmNFKWLAESmSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVGDITEEILADRRHmAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVRRmALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPmILPVVIEG 555
                                    14   |    24        34        44   |    54        64        74        84     |  94       104       114       124       134       144   |   154       164       174       184       194       204       214   |   224       234       244       254       264   |   274       284       294       304       314       324  |    334       344       354       364       374       384       394       404|      414       424       434       444       454       464    |  474       484       494       504   |   514       524       534       544  |    554 
                                        18-MSE                        48-MSE                                    90-MSE                                                   148-MSE                                                               218-MSE                                      263-MSE|                                          313-MSE       327-MSE                                                                       405-MSE  414-MSE                                                469-MSE                                508-MSE                                547-MSE    
                                                                                                                                                                                                                                                                                                 268-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 '\|'

(no "SCOP Domain" information available for 3BK1)

(no "CATH Domain" information available for 3BK1)

(no "Pfam Domain" information available for 3BK1)

Asymmetric Unit(hide GO term definitions)

Chain A (RNJ_THET2 | Q72JJ7)

molecular function
	GO:0004534	5'-3' exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of an RNA molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	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: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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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: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:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:366 - Pro A:367	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3bk1
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	RNJ_THET2 \| Q72JJ7
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	3.-.-.-
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	RNJ_THET2 \| Q72JJ7	:	3bk2 3t3n 3t3o

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (15, 15)

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