2PJP - JenaLib

Title :   STRUCTURE OF THE MRNA-BINDING DOMAIN OF ELONGATION FACTOR SELB FROM E.COLI IN COMPLEX WITH SECIS RNA

Authors :   N. Soler, D. Fourmy, S. Yoshizawa

Date :   16 Apr 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Selb, Protein-Rna Complex, Elongation Factor, Secis, Winged- Helix, Bulge, Translation/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Soler, D. Fourmy, S. Yoshizawa
Structural Insight Into A Molecular Switch In Tandem Winged-Helix Motifs From Elongation Factor Selb.
J. Mol. Biol. V. 370 728 2007
PubMed-ID: 17537456 | Reference-DOI: 10.1016/J.JMB.2007.05.001
(for further references see the PDB file header)

Compounds

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	SELB, FDHA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SELB TRANSLATION FACTOR

Molecule 2 - SECIS RNA
	Chains	:	B
	Engineered	:	YES
	Other Details	:	IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 24)

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:87 , ASP A:504 , TYR A:545	BINDING SITE FOR RESIDUE CL A 98
02	AC3	SOFTWARE	C B:28 , A B:29	BINDING SITE FOR RESIDUE MG B 99
03	AC4	SOFTWARE	HOH A:126 , HOH B:184	BINDING SITE FOR RESIDUE MG A 100
04	AC5	SOFTWARE	HOH A:95 , HOH A:96 , ARG A:592	BINDING SITE FOR RESIDUE CL A 101
05	AC6	SOFTWARE	ASP A:561 , LEU A:605	BINDING SITE FOR RESIDUE CA A 102
06	AC7	SOFTWARE	HOH A:67 , HOH A:68	BINDING SITE FOR RESIDUE MG A 103
07	AC9	SOFTWARE	HOH B:183 , HOH B:201	BINDING SITE FOR RESIDUE MG B 104
08	AD1	SOFTWARE	A B:21	BINDING SITE FOR RESIDUE MG B 105
09	AD2	SOFTWARE	G B:19 , C B:20	BINDING SITE FOR RESIDUE MG B 106
10	AD3	SOFTWARE	HOH A:43 , HOH A:44 , ASP A:519 , ASP A:559	BINDING SITE FOR RESIDUE CA A 49
11	BC1	SOFTWARE	G B:15 , G B:16 , HOH B:170 , HOH B:199	BINDING SITE FOR RESIDUE MG B 150
12	BC2	SOFTWARE	C B:25	BINDING SITE FOR RESIDUE MG B 151
13	BC3	SOFTWARE	C B:30	BINDING SITE FOR RESIDUE MG B 152
14	BC4	SOFTWARE	LEU A:604 , C B:31	BINDING SITE FOR RESIDUE MG B 140
15	BC5	SOFTWARE	HOH A:116 , ARG A:558	BINDING SITE FOR RESIDUE CA A 141
16	BC6	SOFTWARE	G B:19 , HOH B:200	BINDING SITE FOR RESIDUE MG B 142
17	BC7	SOFTWARE	G B:22 , HOH B:179 , HOH B:195	BINDING SITE FOR RESIDUE MG B 143
18	BC8	SOFTWARE	LYS A:581 , ILE A:584 , HOH B:163 , HOH B:197	BINDING SITE FOR RESIDUE MG A 160
19	CC1	SOFTWARE	G B:12 , HOH B:172	BINDING SITE FOR RESIDUE MG B 50
20	CC2	SOFTWARE	HOH A:107 , HOH A:114	BINDING SITE FOR RESIDUE MG B 51
21	CC3	SOFTWARE	G B:16 , U B:18	BINDING SITE FOR RESIDUE MG B 52

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

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Chain A from PDB  Type:PROTEIN  Length:121
 aligned with SELB_ECOLI | P14081 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:121
                                   496       506       516       526       536       546       556       566       576       586       596       606 
           SELB_ECOLI   487 FSEEQQAIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGNDHLLRD 607
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------SelB-wing_3-2pjpA01 A:557-606                     - Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....eehhhhhhhh..hhhhhhhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pjp A 487 FSEEQQAIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGNDHLLRD 607
                                   496       506       516       526       536       546       556       566       576       586       596       606

Chain B from PDB  Type:RNA  Length:23
                                                       
                 2pjp B  12 GGCGGUUGCAGGUCUGCACCGCC  34
                                    21        31

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SELB_ECOLI | P14081)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0035368	selenocysteine insertion sequence binding	Interacting selectively and non-covalently with the selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0001514	selenocysteine incorporation	The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
	GO:0016259	selenocysteine metabolic process	The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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