3BK2 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE RNASE J/UMP COMPLEX

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 :   2.10

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

Keywords :   Rnase J, Endoribonuclease, 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 (5, 21)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION
4	U5P	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 38)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION
4	U5P	2	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:147 , HIS A:186 , ARG A:416 , GOL A:603	BINDING SITE FOR RESIDUE SO4 A 947
2	AC2	SOFTWARE	HIS A:75 , HIS A:77 , HIS A:150 , ASP A:172 , ZN A:949	BINDING SITE FOR RESIDUE ZN A 948
3	AC3	SOFTWARE	ASP A:79 , HIS A:80 , ASP A:172 , HIS A:398 , ZN A:948	BINDING SITE FOR RESIDUE ZN A 949
4	AC4	SOFTWARE	ILE A:21 , GLU A:78 , ASP A:79 , PHE A:240 , HIS A:243 , SER A:340 , PRO A:341 , ILE A:342 , PRO A:343 , HIS A:372 , SER A:374 , GLY A:375 , HIS A:376 , HOH A:957 , HOH A:964 , HOH A:1103 , HOH A:1116	BINDING SITE FOR RESIDUE U5P A 950
5	AC5	SOFTWARE	GLN A:379 , ASN A:406	BINDING SITE FOR RESIDUE GOL A 601
6	AC6	SOFTWARE	LYS A:222 , ASP A:225 , TRP A:252 , HOH A:1107	BINDING SITE FOR RESIDUE GOL A 602
7	AC7	SOFTWARE	HIS A:186 , ALA A:195 , SO4 A:947 , HOH A:1061 , HOH A:1101	BINDING SITE FOR RESIDUE GOL A 603

(no "SS Bond" information available for 3BK2)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3BK2)

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 3BK2)

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:549
 aligned with RNJ_THET2 | Q72JJ7 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:549
                                    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       564         
            RNJ_THET2    25 QDHVEIIPLGGMGEIGKNITVFRFRDEIFVLDGGLAFPEEGMPGVDLLIPRVDYLIEHRHKIKAWVLTHGHEDHIGGLPFLLPMIFGKESPVPIYGARLTLGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRMTHSIPDNSGVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADATNAERPGYTPSEMEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRKVAMEGRSMLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILATGSQGQPMSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQMNFKWLAESMSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVGDITEEILADRRHMAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVRRMALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPMILPVVIEG 573
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhh.......eeeee....eeee...eeeeeee........eeeeeee..eeeee.................hhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh...........hhhhh..hhh.eeeee......hhhhhhhhhh............eeee.......hhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeee....eeeeee....eeeee..eeeeehhhhhhhhhhhhhhheeeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUGAR_TRANSPORT_1 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bk2 A   7 QDHVEIIPLGGmGEIGKNITVFRFRDEIFVLDGGLAFPEEGmPGVDLLIPRVDYLIEHRHKIKAWVLTHGHEDHIGGLPFLLPmIFGKESPVPIYGARLTLGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRmTHSIPDNSGVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADATNAERPGYTPSEmEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRKVAmEGRSmLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILATGSQGQPmSVLHRLAFEGHAKmAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQmNFKWLAESmSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVGDITEEILADRRHmAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVRRmALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPmILPVVIEG 555
                                    16 |      26        36        46 |      56        66        76        86   |    96       106       116       126       136       146 |     156       166       176       186       196       206       216 |     226       236       246       256      |266 |     276       286       296       306      |316       326|      336       346       356       366       376       386       396       406       416       426       436       446       456       466  |    476       486       496       506 |     516       526       536       546|        
                                      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 3BK2)

(no "CATH Domain" information available for 3BK2)

(no "Pfam Domain" information available for 3BK2)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		U5P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3bk2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNJ_THET2 \| Q72JJ7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.-.-.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RNJ_THET2 \| Q72JJ7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RNJ_THET2 \| Q72JJ7	:	3bk1 3t3n 3t3o

3bk1	CRYSTAL STRUCTURE OF FREE RNASE J

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File