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Title :   STRUCTURE OF THE RNA BINDING DOMAIN OF THE BACILLUS SUBTILIS YXIN PROTEIN COMPLEXED WITH A FRAGMENT OF 23S RIBOSOMAL RNA

Authors :   J. W. Hardin, Y. Hu, D. B. Mckay

Date :   22 Apr 10 (Deposition) - 04 Aug 10 (Release) - 06 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Rna, Rna Recognition Motif, Rna Binding Protein, Ribosomal Rna, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Hardin, Y. X. Hu, D. B. Mckay
Structure Of The Rna Binding Domain Of A Dead-Box Helicase Bound To Its Ribosomal Rna Target Reveals A Novel Mode Of Recognition By An Rna Recognition Motif.
J. Mol. Biol. V. 402 412 2010
PubMed-ID: 20673833 | Reference-DOI: 10.1016/J.JMB.2010.07.040
(for further references see the PDB file header)

Compounds

Molecule 1 - RNA (69-MER)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	E. COLI 23 S RIBOSOMAL RNA (NUCLEOTIDES 2508-2580 WITH GAAA TETRALOOP IN NUCLEOTIDES 2530-2533 AND A2581 AT 3' END)
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - ATP-DEPENDENT RNA HELICASE DBPA
	Chains	:	B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL23(DE3)
	Expression System Taxid	:	562
	Gene	:	DBPA, DEAD, YXIN, BSU39110, SS8E
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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)
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Chain A from PDB  Type:RNA  Length:69
                                                                                                      
                3moj A 2508 GGCUCAUCACAUCCUGGGGCUGGAAACGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUAGCUA 2581
                                  2517      2527      2537      2547      2557      2567   ||    
                                                                                        2571|    
                                                                                         2577

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with DBPA_BACSU | P42305 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:75
                                   413       423       433       443       453       463       473     
          DBPA_BACSU    404 MKLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNGKGPHVLKVMKNTTVKGKQLKVNKAN  478
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains DbpA-3mojB01 B:404-477                                                    - Pfam domains
         Sec.struct. author .eeee..hhhhh.hhhhhhhhhhh....hhh.eeeeee....eeeee...hhhhhhhhhh..........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                3moj B  404 MKLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNGKGPHVLKVMKNTTVKGKQLKVNKAN  478
                                   413       423       433       443       453       463       473

Legend:		→ Mismatch	(orange background)
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	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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain B (DBPA_BACSU | P42305)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0034459	ATP-dependent 3'-5' RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix in the direction 3' to 5'.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
biological process
	GO:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	GO:0000027	ribosomal large subunit assembly	The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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