1HRU - JenaLib

Title :   THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI

Authors :   M. Teplova, V. Tereshko, R. Sanishvili, A. Joachimiak, T. Bushueva, W. F. Anderson, M. Egli, Midwest Center For Structural Genomics (Mcsg)

Date :   21 Dec 00 (Deposition) - 31 Jan 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein Folding, Structural Genomics, Rna, Sua5, Yrdc, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Teplova, V. Tereshko, R. Sanishvili, A. Joachimiak, T. Bushueva, W. F. Anderson, M. Egli
The Structure Of The Yrdc Gene Product From Escherichia Coli Reveals A New Fold And Suggests A Role In Rna Binding.
Protein Sci. V. 9 2557 2000
PubMed-ID: 11206077
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:186
 aligned with TSAC_ECOLI | P45748 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           TSAC_ECOLI     3 NNLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKPYIDDTMLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVVPGETGGRLNPSEIRDALTGELFR 188
               SCOP domains d1hrua_ A: Hypothetical protein YrdC                                                                                                                                                       SCOP domains
               CATH domains 1hruA00 A:3-188 DHBP synthase                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeee....eeeee...hhhhhhhhhhhhh.hhhhh.eeee.hhhhhhhhh.....hhhhhhhhhh.....eeeeee.....hhhhhh...eeeeee..hhhhhhhhhhhh..eeeee..........hhhhhhhhhh.................eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----YRDC  PDB: A:7-188 UniProt: 7-190                                                                                                                                                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hru A   3 NNLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVmRLLELKQRPVDKGLILIAANYEQLKPYIDDTmLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVVPGETGGRLNPSEIRDALTGELFR 188
                                    12        22        32        42 |      52        62        72   |    82        92       102       112       122       132       142       152       162       172       182      
                                                                    44-MSE                          76-MSE

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with TSAC_ECOLI | P45748 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:184
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
           TSAC_ECOLI     4 NLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKPYIDDTMLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVVPGETGGRLNPSEIRDALTGELF 187
               SCOP domains d1hrub_ B: Hypothetical protein YrdC                                                                                                                                                     SCOP domains
               CATH domains 1hruB00 B:204-387 DHBP synthase                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeee....eeeee...hhhhhhhhhhhhh.hhhhh.eeee.hhhhhhhhh.....hhhhhhhhhh......eeeee.....hhhhhh...eeeeee..hhhhhhhhhhhh..eeeee..........hhhhhhhhhh..................eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---YRDC  PDB: B:207-387 UniProt: 7-190                                                                                                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hru B 204 NLQRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVmRLLELKQRPVDKGLILIAANYEQLKPYIDDTmLTDVQRETIFSRWPGPVTFVFPAPATTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVVPGETGGRLNPSEIRDALTGELF 387
                                   213       223       233       243|      253       263       273  |    283       293       303       313       323       333       343       353       363       373       383    
                                                                  244-MSE                         276-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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TSAC_ECOLI | P45748)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0061710	L-threonylcarbamoyladenylate synthase	Catalysis of the reaction: L-threonine + ATP + bicarbonate = L-threonylcarbamoyladenylate + diphosphate + H(2)O.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	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.
	GO:0002949	tRNA threonylcarbamoyladenosine modification	The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Visualization

Interactive Views

Asymmetric/Biological 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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:174 - Pro A:175	[ RasMol ]
		Trp A:89 - Pro A:90	[ RasMol ]
		Trp B:289 - Pro B:290	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1hru
		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
	TSAC_ECOLI \| P45748
		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)
	(no 'Enzyme Classificator' available)
		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

Description