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(-) Description

Title :  A NEW MGGDP COMPLEX OF THE FFH NG DOMAIN
 
Authors :  D. M. Freymann
Date :  25 Nov 02  (Deposition) - 02 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Transport, Ffh, Signal Recognition Particle, Srp, Gtpase, Gtp-Binding, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Focia, H. Alam, T. Lu, U. D. Ramirez, D. M. Freymann
Novel Protein And Mg2+ Configurations In The Mg2+Gdp Complex Of The Srp Gtpase Ffh
Proteins: Struct. , Funct. , V. 54 222 2004 Genet.
PubMed-ID: 14696184  |  Reference-DOI: 10.1002/PROT.10598

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NG GTPASE DOMAIN, RESIDUES 1-296
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: FIFTY-FOUR HOMOLOG, FFH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FMT5Ligand/IonFORMIC ACID
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT2Ligand/IonFORMIC ACID
3GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT3Ligand/IonFORMIC ACID
3GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:32 , ARG A:36BINDING SITE FOR RESIDUE CL A1296
02AC2SOFTWARETHR A:112 , GDP A:1299 , HOH A:2055 , HOH A:2074 , HOH A:2127 , HOH A:2128BINDING SITE FOR RESIDUE MG A1300
03AC3SOFTWAREASP A:212 , HOH A:2090 , HOH A:2091 , HOH A:2092BINDING SITE FOR RESIDUE MG A1301
04AC4SOFTWARETHR B:112 , GDP B:1299 , HOH B:2067 , HOH B:2098 , HOH B:2143BINDING SITE FOR RESIDUE MG B1300
05AC5SOFTWAREASP B:212 , HOH B:2116 , HOH B:2117BINDING SITE FOR RESIDUE MG B1301
06AC6SOFTWARELEU A:106 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , LYS A:117 , GLN A:144 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , MG A:1300 , HOH A:2056 , HOH A:2127 , HOH A:2128 , HOH A:2129BINDING SITE FOR RESIDUE GDP A1299
07AC7SOFTWARELEU B:106 , GLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112 , THR B:113 , LYS B:117 , LYS B:246 , ASP B:248 , GLY B:271 , VAL B:272 , SER B:273 , GLU B:274 , MG B:1300 , HOH B:2060 , HOH B:2061 , HOH B:2070 , HOH B:2143BINDING SITE FOR RESIDUE GDP B1299
08AC8SOFTWAREPRO A:281 , ARG A:286 , SER B:67 , THR B:69 , VAL B:73BINDING SITE FOR RESIDUE FMT A1297
09AC9SOFTWAREARG A:191 , GLN A:193 , ASP A:195 , LEU A:198 , MET A:199BINDING SITE FOR RESIDUE FMT A1298
10BC1SOFTWARETYR B:79 , GLU B:285 , HOH B:2141BINDING SITE FOR RESIDUE FMT B1296
11BC2SOFTWARESER A:67 , THR A:69 , VAL A:73 , PRO B:281 , ARG B:286 , HOH B:2134 , HOH B:2142BINDING SITE FOR RESIDUE FMT B1297
12BC3SOFTWAREARG B:191 , LEU B:192 , GLN B:193BINDING SITE FOR RESIDUE FMT B1298

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O87)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O87)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O87)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1O87)

(-) Sequences/Alignments

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: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 d1o87a1 A:1-88 Signal sequence recognition protein Ffh                                  d1o87a2 A:89-295 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                   SCOP domains
               CATH domains -1o87A01 A:2-90  [code=1.20.120.140, no name defined]                                     1o87A02 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......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o87 A   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     


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 d1o87b1 B:1-88 Signal sequence recognition protein Ffh                                  d1o87b2 B:89-295 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                   SCOP domains
               CATH domains -1o87B01 B:2-90  [code=1.20.120.140, no name defined]                                     1o87B02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          -------------- CATH domains
           Pfam domains (1) ----SRP54_N-1o87B03 B:5-82                                                        ---------------SRP54-1o87B01 B:98-293                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) ----SRP54_N-1o87B04 B:5-82                                                        ---------------SRP54-1o87B02 B:98-293                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...........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
                 1o87 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: SRP54 (20)
(-)
Thermus aquaticus (12)
1aSRP54-1o87B01B:98-293
1bSRP54-1o87B02B:98-293
(-)
Clan: no clan defined [family: SRP54_N] (20)

(-) Gene Ontology  (11, 11)

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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  1o87
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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
        SRP54_THEAQ | O07347: 1ffh 1jpj 1jpn 1ls1 1ng1 1okk 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 RECOGNITIONPROTEIN 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 RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
2ffh THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUSAQUATICUS
2ng1 N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
3ng1 N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS