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(-) Description

Title :  HOMO-HETERODIMERIC COMPLEX OF THE SRP GTPASES
 
Authors :  P. J. Focia, D. M. Freymann
Date :  26 Jul 03  (Deposition) - 19 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Cell Cycle, Signal Recognition/Complex, Srp, Ffh, Ftsy, Gtpase, Membrane Targeting, Signal Sequence Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Focia, I. V. Shepotinovskaya, J. A. Seidler, D. M. Freymann
Heterodimeric Gtpase Core Of The Srp Targeting Complex
Science V. 303 373 2004
PubMed-ID: 14726591  |  Reference-DOI: 10.1126/SCIENCE.1090827
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NG DOMAIN, RESIDUES 0-293
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: FIFTY-FOUR HOMOLOG, FFH
 
Molecule 2 - CELL DIVISION PROTEIN FTSY
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NG DOMAIN, RESIDUES 2-304
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1BZP2Ligand/IonN1-CARBOXYPIPERAZINE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GCP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
4MG2Ligand/IonMAGNESIUM ION
5SO411Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:21 , HOH A:2344 , HOH A:2345 , HOH A:2346 , HOH A:2347 , VAL D:160 , ILE D:161 , GLN D:162 , HOH D:2102BINDING SITE FOR RESIDUE SO4 A1298
02AC2SOFTWAREARG A:32 , ARG A:35 , ARG A:49 , HOH A:2349BINDING SITE FOR RESIDUE SO4 A1299
03AC3SOFTWAREALA A:140 , ALA A:141 , ARG A:142 , GLU A:143 , HOH A:2202BINDING SITE FOR RESIDUE SO4 A1300
04AC4SOFTWARELYS A:28 , ARG A:286 , ARG A:290 , HOH A:2350 , HOH A:2351 , HOH A:2352BINDING SITE FOR RESIDUE SO4 A1301
05AC5SOFTWARESER A:67 , LEU A:68 , THR A:69 , HOH A:2353 , HOH A:2354 , LYS D:132 , ARG D:183 , TYR D:185BINDING SITE FOR RESIDUE SO4 A1302
06AC6SOFTWARESER A:164 , SER A:167 , ARG A:170 , HOH A:2355BINDING SITE FOR RESIDUE SO4 A1303
07AC7SOFTWAREARG A:128 , ARG A:181BINDING SITE FOR RESIDUE SO4 A1304
08AC8SOFTWAREARG A:169 , ARG A:170 , HOH A:2356BINDING SITE FOR RESIDUE SO4 A1305
09AC9SOFTWAREARG A:231 , HOH A:2357 , LYS D:207 , ARG D:211BINDING SITE FOR RESIDUE SO4 A1306
10BC1SOFTWAREARG A:142 , MET A:160 , ASP A:161BINDING SITE FOR RESIDUE SO4 A1307
11BC2SOFTWAREARG D:124 , ARG D:155 , PRO D:286 , HOH D:2209BINDING SITE FOR RESIDUE SO4 D1308
12BC3SOFTWARETHR A:112 , GCP A:1001 , HOH A:2196 , HOH A:2207 , HOH A:2249BINDING SITE FOR RESIDUE MG A1002
13BC4SOFTWARETHR D:116 , GCP D:1001 , HOH D:2082 , HOH D:2123 , HOH D:2207BINDING SITE FOR RESIDUE MG D1002
14BC5SOFTWAREGLN A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , LYS A:117 , ASP A:135 , ARG A:138 , GLN A:144 , GLY A:190 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , MG A:1002 , HOH A:2181 , HOH A:2182 , HOH A:2196 , HOH A:2197 , HOH A:2207 , HOH A:2249 , HOH A:2342 , ASN D:111 , ARG D:142 , LEU D:196 , GCP D:1001 , HOH D:2065BINDING SITE FOR RESIDUE GCP A1001
15BC6SOFTWAREALA A:270 , GLU A:280 , PRO A:281 , PHE A:282 , TYR A:283 , ARG A:286 , ARG A:290BINDING SITE FOR RESIDUE BZP A1296
16BC7SOFTWARELYS A:96 , ASP A:97 , ARG A:98 , LYS A:206 , HOH A:2175BINDING SITE FOR RESIDUE BZP A1297
17BC8SOFTWAREGLN A:107 , ARG A:138 , GCP A:1001 , ASN D:111 , GLY D:112 , VAL D:113 , GLY D:114 , LYS D:115 , THR D:116 , THR D:117 , LYS D:121 , ARG D:142 , GLN D:148 , GLY D:194 , LYS D:256 , ASP D:258 , GLY D:281 , VAL D:282 , GLY D:283 , GLU D:284 , MG D:1002 , HOH D:2067 , HOH D:2082 , HOH D:2085 , HOH D:2123 , HOH D:2207 , HOH D:2208BINDING SITE FOR RESIDUE GCP D1001
18BC9SOFTWARELEU A:106 , GLN A:193 , VAL D:231 , GLY D:259 , THR D:260 , ALA D:261 , HOH D:2172BINDING SITE FOR RESIDUE EDO D1309
19CC1SOFTWAREARG A:127 , LYS D:215 , EDO D:1311BINDING SITE FOR RESIDUE EDO D1310
20CC2SOFTWARETYR D:174 , LYS D:215 , EDO D:1310BINDING SITE FOR RESIDUE EDO D1311
21CC3SOFTWAREGLU D:151 , TRP D:152 , ARG D:155 , HOH D:2210 , HOH D:2211BINDING SITE FOR RESIDUE EDO D1312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_THEAQ266-279  1A:266-279
FTSY_THEAQ276-289  1D:276-289

(-) Exons   (0, 0)

(no "Exon" information available for 1OKK)

(-) 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:290
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:290
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
          SRP54_THEAQ     4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILG 293
               SCOP domains d1okka1 A:4-88 Signal sequence recognition protein Ffh                               d1okka2 A:89-293 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                 SCOP domains
               CATH domains 1okkA01 A:4-90  [code=1.20.120.140, no name defined]                                   1okkA02 A:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ------------ CATH domains
               Pfam domains -SRP54_N-1okkA02 A:5-82                                                        ---------------SRP54-1okkA01 A:98-293                                                                                                                                                                               Pfam domains
         Sec.struct. author ..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeee........hhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         -------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okk A   4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILG 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293


Chain D from PDB  Type:PROTEIN  Length:265
 aligned with FTSY_THEAQ | P83749 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:283
                                    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   
           FTSY_THEAQ    21 AIPWGGNLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLE 303
               SCOP domains d1okkd1 D:21-78 Signal recognition particle receptor, FtsY------------------d1okkd2 D:97-303 GTPase domain of the signal recognition particle receptor FtsY                                                                                                                                 SCOP domains
               CATH domains 1okkD01 D:21-78  [code=1.20.120.140, no name defined]     ------------------1okkD02 D:97-303 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
               Pfam domains SRP54_N-1okkD02 D:21-77                                  ------------------------SRP54-1okkD01 D:102-303                                                                                                                                                                                    Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhh..------------------.......eeeee.....hhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh..eeeee.......eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         -------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okk D  21 AIPWGGNLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEP------------------PVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLE 303
                                    30        40        50        60        70       | -         -      |100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   
                                                                                    78                 97
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: SRP54 (20)
(-)
Thermus aquaticus (12)
1aSRP54-1okkD01D:102-303
1bSRP54-1okkA01A:98-293
(-)
Clan: no clan defined [family: SRP54_N] (20)

(-) Gene Ontology  (14, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain D   (FTSY_THEAQ | P83749)
molecular function
    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: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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  SRP54_THEAQ | O07347
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FTSY_THEAQ | P83749: 1rj9 2cnw 2iyl 2j7p 2q9a 2q9b 2q9c 2xkv
        SRP54_THEAQ | O07347: 1ffh 1jpj 1jpn 1ls1 1ng1 1o87 1rj9 1ry1 2c03 2c04 2cnw 2ffh 2iy3 2j45 2j46 2j7p 2ng1 2xkv 3ng1 3zn8

(-) Related Entries Specified in the PDB File

1ffh N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS
1jpj GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN
1jpn GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN
1ls1 T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
1ng1 N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS
1o87 A NEW MGGDP COMPLEX OF THE FFH NG DOMAIN
1rj9 STRUCTURE OF THE HETERODIMER OF THE CONSERVED GTPASEDOMAINS OF THE SIGNAL RECOGNITION PARTICLE (FFH) AND ITS RECEPTOR (FTSY)
2ffh THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS
2ng1 N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS
3ng1 N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS