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Title :   GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN

Authors :   S. Padmanabhan, D. M. Freymann

Date :   02 Aug 01 (Deposition) - 02 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ffh, Srp, Gmppnp, Signal Recognition Particle, Srp54, Ng Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Padmanabhan, D. M. Freymann
The Conformation Of Bound Gmppnp Suggests A Mechanism For Gating The Active Site Of The Srp Gtpase.
Structure V. 9 859 2001
PubMed-ID: 11566135 | Reference-DOI: 10.1016/S0969-2126(01)00641-4
(for further references see the PDB file header)

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
	Chains	:	B, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NG DOMAIN
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	FIFTY-FOUR HOMOLOG

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:		B
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	CA	2	Ligand/Ion	CALCIUM ION
3	GNP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1492 , HOH A:1494 , HOH A:1495 , GLU B:46 , GLU B:207 , HOH B:1493	BINDING SITE FOR RESIDUE CA B 900
2	AC2	SOFTWARE	GLU A:46 , GLU A:207 , HOH A:1496 , HOH A:1497 , HOH A:1498 , GLU B:72	BINDING SITE FOR RESIDUE CA A 901
3	AC3	SOFTWARE	LEU B:106 , GLN B:107 , GLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112 , THR B:113 , GLN B:144 , LYS B:246 , ASP B:248 , GLY B:271 , VAL B:272 , SER B:273 , GLU B:274	BINDING SITE FOR RESIDUE GNP B 910
4	AC4	SOFTWARE	LEU A:106 , GLN A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , GLN A:144 , GLY A:190 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , HOH A:1435	BINDING SITE FOR RESIDUE GNP A 911
5	AC5	SOFTWARE	ALA B:133 , ALA B:134 , ASP B:135 , ALA B:141 , LEU B:145 , ASP B:187 , THR B:188	BINDING SITE FOR RESIDUE ACY B 950
6	AC6	SOFTWARE	PRO B:281 , TYR B:283	BINDING SITE FOR RESIDUE ACY B 951
7	AC7	SOFTWARE	ALA A:133 , ALA A:134 , ASP A:135 , ALA A:141 , ARG A:142 , ASP A:187 , THR A:188 , HOH A:1161	BINDING SITE FOR RESIDUE ACY A 952
8	AC8	SOFTWARE	ARG A:231 , ASP A:234 , GLU A:235 , THR A:263 , HOH A:1370	BINDING SITE FOR RESIDUE ACY A 953

(no "SS Bond" information available for 1JPN)

(no "Cis Peptide Bond" information available for 1JPN)

(no "SAP(SNP)/Variant" information available for 1JPN)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_THEAQ	266-279	2	A:266-279 B:266-279

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_THEAQ	266-279	1	- B:266-279

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_THEAQ	266-279	1	A:266-279 -

(no "Exon" information available for 1JPN)

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:296
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:296
                                    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      
          SRP54_THEAQ     1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
               SCOP domains d1jpna1 A:1-88 Signal sequence recognition protein Ffh                                  d1jpna2 A:89-296 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                    SCOP domains
               CATH domains -1jpnA01 A:2-90  [code=1.20.120.140, no name defined]                                     1jpnA02 A:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ----------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpn A   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
                                    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

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:295
                                    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     
          SRP54_THEAQ     1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
               SCOP domains d1jpnb1 B:1-88 Signal sequence recognition protein Ffh                                  d1jpnb2 B:89-295 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                   SCOP domains
               CATH domains -1jpnB01 B:2-90  [code=1.20.120.140, no name defined]                                     1jpnB02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          -------------- CATH domains
           Pfam domains (1) ----SRP54_N-1jpnB03 B:5-82                                                        ---------------SRP54-1jpnB01 B:98-293                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) ----SRP54_N-1jpnB04 B:5-82                                                        ---------------SRP54-1jpnB02 B:98-293                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpn B   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
                                    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

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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: SRP54 (20)

Thermus aquaticus (12)

1a	SRP54-1jpnB01	B:98-293
1b	SRP54-1jpnB02	B:98-293

Clan: no clan defined [family: SRP54_N] (20)

Family: SRP54_N (20)

Thermus aquaticus (12)

2a	SRP54_N-1jpnB03	B:5-82
2b	SRP54_N-1jpnB04	B:5-82

Asymmetric Unit(hide GO term definitions)

Chain A,B (SRP54_THEAQ | O07347)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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1jpj	1JPJ CONTAINS THE SAME PROTEIN WITH DIFFERENT HET GROUPS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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