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(-) Description

Title :  STRUCTURE OF THE GTP-BINDING PROTEIN TRME FROM THERMOTOGA MARITIMA COMPLEXED WITH 5-FORMYL-THF
 
Authors :  A. Scrima, I. R. Vetter, M. E. Armengod, A. Wittinghofer
Date :  12 Nov 04  (Deposition) - 04 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Gtp-Binding, Thf-Binding, Trna-Modification, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Scrima, I. R. Vetter, M. E. Armengod, A. Wittinghofer
The Structure Of The Trme Gtp-Binding Protein And Its Implications For Trna Modification
Embo J. V. 24 23 2005
PubMed-ID: 15616586  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600507
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE TRNA MODIFICATION GTPASE TRME
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21DE3 (TRME-)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRME
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRME GTP-BINDING PROTEIN
 
Molecule 2 - PROBABLE TRNA MODIFICATION GTPASE TRME
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21DE3 (TRME-)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (RESIDUES 1-117)
    Gene: TRME
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRME GTP-BINDING PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FON2Ligand/IonFOLINIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FON2Ligand/IonFOLINIC ACID
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1FON4Ligand/IonFOLINIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:20 , LYS A:69 , SER A:70 , TYR A:71 , GLU A:78 , LYS A:117 , LYS A:450 , ILE B:16 , HIS B:47 , GLU B:59 , VAL B:61 , MET B:80BINDING SITE FOR RESIDUE FON A 451
2AC2SOFTWAREILE A:16 , HIS A:47 , GLU A:59 , VAL A:61 , MET A:80 , HIS A:82 , ARG B:20 , ARG B:43 , PRO B:68 , LYS B:69 , SER B:70 , TYR B:71 , GLU B:78BINDING SITE FOR RESIDUE FON B 118

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TRMEPS51709 TrmE-type guanine nucleotide-binding (G) domain profile.MNME_THEMA211-372  1A:211-372
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TRMEPS51709 TrmE-type guanine nucleotide-binding (G) domain profile.MNME_THEMA211-372  1A:211-372
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TRMEPS51709 TrmE-type guanine nucleotide-binding (G) domain profile.MNME_THEMA211-372  2A:211-372

(-) Exons   (0, 0)

(no "Exon" information available for 1XZQ)

(-) 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:449
 aligned with MNME_THEMA | Q9WYA4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:449
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441         
           MNME_THEMA     2 DTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK 450
               SCOP domains d1xzqa3 A:2-117 TrmE formyl-THF-binding domain                                                                      d1xzqa1 A:118-211,A:372-450 TrmE connector domain                                             d1xzqa2 A:212-371 TrmE GTPase domain                                                                                                                            d1xzqa1 A:118-211,A:372-450 TrmE connector domain                               SCOP domains
               CATH domains 1xzqA01 A:2-117 Probable tRNA modification gtpase trme; domain 1                                                    1xzqA02 A:118-211,A:379-450 Probable tRNA modification gtpase trme. Chain:  A, domain 2       1xzqA03 A:212-378 P-loop containing nucleotide triphosphate hydrolases                                                                                                 1xzqA02 A:118-211,A:379-450                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MMR_HSR1-1xzqA01 A:213-327                                                                                         -----------------------------------------------GTPase_Cys_C-1xzqA02 A:375-447                                           --- Pfam domains
         Sec.struct. author ..eeee.........eeeeee..hhhhhhhh..........................eeeeeee..........eeeeee..hhhhhhhhhhhhhh........hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhheeeeee....hhhhhhhhhhhhhh................eeeee..eeeeeee...............hhhhhhhhh....eeeeeee.....hhhhhhhhhhhh...eeeeeee.......hhhhhhhhh.....eeeee.....hhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_TRME  PDB: A:211-372 UniProt: 211-372                                                                                                                           ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xzq A   2 DTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK 450
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441         


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with MNME_THEMA | Q9WYA4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           MNME_THEMA     1 MDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGK 117
               SCOP domains d1xzqb1 B:1-117 TrmE formyl-THF-binding domain                                                                        SCOP domains
               CATH domains 1xzqB00 B:1-117 Probable tRNA modification gtpase trme; domain 1                                                      CATH domains
           Pfam domains (1) --TrmE_N-1xzqB01 B:3-117                                                                                              Pfam domains (1)
           Pfam domains (2) --TrmE_N-1xzqB02 B:3-117                                                                                              Pfam domains (2)
         Sec.struct. author ...eeee........eeeeeee..hhhhhhhh.............eeeee......eeeeeeeee..........eeeeeee.hhhhhhhhhhhhhh........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1xzq B   1 MDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGK 117
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (3, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (3, 4)

Asymmetric Unit
(-)
Clan: FBD (14)
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTPase_Cys_C] (2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MNME_THEMA | Q9WYA4)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
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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  1xzq
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 Related Entries

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

UniProtKB/Swiss-Prot
        MNME_THEMA | Q9WYA4: 1xzp

(-) Related Entries Specified in the PDB File

1xzp THE GTP-BINDING PROTEIN TRME