3KL4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   RECOGNITION OF A SIGNAL PEPTIDE BY THE SIGNAL RECOGNITION PARTICLE

Authors :   C. Y. Janda, K. Nagai, J. Li, C. Oubridge

Date :   06 Nov 09 (Deposition) - 31 Mar 10 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Signal Recognition Particle, Srp, Srp54, Ffh, Signal Sequence, Signal Peptide, Gtp-Binding, Nucleotide-Binding, Ribonucleoprotein, Rna- Binding, Signal-Anchor, Transmembrane, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Y. Janda, J. Li, C. Oubridge, H. Hernandez, C. V. Robinson, K. Nagai
Recognition Of A Signal Peptide By The Signal Recognition Particle.
Nature V. 465 507 2010
PubMed-ID: 20364120 | Reference-DOI: 10.1038/NATURE08870
(for further references see the PDB file header)

Molecule 1 - SIGNAL RECOGNITION 54 KDA PROTEIN
	Chains	:	A
	EC Number	:	3.6.5.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 2-432
	Gene	:	SRP54, SSO0971
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	P2
	Synonym	:	SRP54

Molecule 2 - SIGNAL PEPTIDE OF YEAST DIPEPTIDYL AMINOPEPTIDASE B
	Chains	:	B
	EC Number	:	3.4.14.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-51
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	DPAP B, YSCV

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3KL4)

(no "Site" information available for 3KL4)

(no "SS Bond" information available for 3KL4)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:95	-	Pro A:96

(no "SAP(SNP)/Variant" information available for 3KL4)

(no "PROSITE Motif" information available for 3KL4)

(no "Exon" information available for 3KL4)

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:413
 aligned with SRP54_SULSO | Q97ZE7 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430  
          SRP54_SULSO     1 MLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESILEKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGIMLPTPSEDQLKIGEEKIRRWLAALNSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNNMNRLLKMVK 432
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -SRP54_N-3kl4A02 A:2-78                                                       -----------------SRP54-3kl4A01 A:96-293                                                                                                                                                                                ---------------------------------SRP_SPB-3kl4A03 A:327-428                                                                             ---- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.............eeeee......hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh....ee......hhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeehhhhh.hhhhhhhhhhhhh.eeeeee.......eee.hhhhhhhhhhh.hhhhhhhhhhhhh-------------------.hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kl4 A   1 GLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESILEKVKGL-------------------LTLRDVYAQIIALRKMGPLSKVLQHIPGLGIMLPTPSEDQLKIGEEKIRRWLAALNSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNNMNRLLKMVK 432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      |  -         -      |330       340       350       360       370       380       390       400       410       420       430  
                                                                                                                                                                                                                                                                                                                                            307                 327

Chain B from PDB  Type:PROTEIN  Length:21
 aligned with DAP2_YEAST | P18962 from UniProtKB/Swiss-Prot  Length:818

    Alignment length:21
                                    40        50 
           DAP2_YEAST    31 GIILVLLIWGTVLLLKSIPHH  51
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 3kl4 B 449 GIILVLLIWGTVLLLKSIPHH 469
                                   458       468

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 3KL4)

(no "CATH Domain" information available for 3KL4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SRP54_SULSO | Q97ZE7)

molecular function
	GO:0008312	7S RNA binding	Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
	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.
biological process
	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.

Chain B (DAP2_YEAST | P18962)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	GO:0008239	dipeptidyl-peptidase activity	Catalysis of the hydrolysis of N-terminal dipeptides from a polypeptide chain.
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0000329	fungal-type vacuole membrane	The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3kl4)

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(no "Sites" information available for 3kl4)

	Cis Peptide Bonds
		Leu A:95 - Pro A:96	[ RasMol ]

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	SRP54_SULSO \| Q97ZE7
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	3.4.14.-
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	3.6.5.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
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UniProtKB/Swiss-Prot
	DAP2_YEAST \| P18962	:	3zn8
	SRP54_SULSO \| Q97ZE7	:	1qzw 1qzx 2iy3 3zn8 5l3s 5l3v

1dul	CRYSTAL STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE SIGNAL RECOGNITION PARTICLE.
1j8m	THE CRYSTAL STRUCTURE OF THE CONSERVED GTPASE OF SRP54 FROM THE ARCHAEON ACIDIANUS AMBIVALENS AND ITS COMPARISON WITH RELATED STRUCTURES SUGGESTS A MODEL FOR THE SRP-SRP RECEPTOR COMPLEX.
1qzw	CRYSTAL STRUCTURE OF THE COMPLETE CORE OF ARCHAEAL SIGNAL RECOGNITION PARTICLE AND IMPLICATIONS FOR INTERDOMAIN COMMUNICATION.
1qzx	CRYSTAL STRUCTURE OF THE COMPLETE CORE OF ARCHAEAL SIGNAL RECOGNITION PARTICLE AND IMPLICATIONS FOR INTERDOMAIN COMMUNICATION.
2ffh	CRYSTAL STRUCTURE OF THE SIGNAL SEQUENCE BINDING SUBUNIT OF THE SIGNAL RECOGNITION PARTICLE.
2j28	FOLLOWING THE SIGNAL SEQUENCE FROM RIBOSOMAL TUNNEL EXIT TO SIGNAL RECOGNITION PARTICLE.

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (3, 3)

Gene Ontology (23, 23)

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