1XZP - JenaLib

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Title :   STRUCTURE OF THE GTP-BINDING PROTEIN TRME FROM THERMOTOGA MARITIMA

Authors :   A. Scrima, I. R. Vetter, M. E. Armengod, A. Wittinghofer

Date :   12 Nov 04 (Deposition) - 04 Jan 05 (Release) - 31 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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)

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 1-118)
	Gene	:	TRME
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	TRME GTP-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 10)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:230 , GLY A:359 , LEU A:360 , GLU A:361 , ARG A:435 , HOH A:1069	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	ARG A:210 , ARG A:213 , ARG A:262	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	ILE B:16 , GLU B:59 , VAL B:61 , MET B:80 , CYS B:81	BINDING SITE FOR RESIDUE SO4 B 1003
4	AC4	SOFTWARE	LYS A:13 , ARG B:20 , GLY B:106 , GLU B:107 , PHE B:108 , THR B:109 , HOH B:1045	BINDING SITE FOR RESIDUE SO4 B 1004
5	AC5	SOFTWARE	LYS A:327 , GLU A:332 , LYS A:351 , LYS A:356 , GLN A:390 , HOH A:1047	BINDING SITE FOR RESIDUE SO4 A 1005

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_THEMA	211-372	1	A:211-372

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_THEMA	211-372	1	A:211-372

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_THEMA	211-372	2	A:211-372

(no "Exon" information available for 1XZP)

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:456
 aligned with MNME_THEMA | Q9WYA4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:456
                                  1                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444      
           MNME_THEMA     - ------MDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK 450
               SCOP domains ------d1xzpa3 A:1-117 TrmE formyl-THF-binding domain                                                                       d1xzpa1 A:118-211,A:372-450 TrmE connector domain                                             d1xzpa2 A:212-371 TrmE GTPase domain                                                                                                                            d1xzpa1 A:118-211,A:372-450 TrmE connector domain                               SCOP domains
               CATH domains 1xzpA01 A:-5-117 Probable tRNA modification gtpase trme; domain 1                                                          1xzpA02 A:118-211,A:379-450 Probable tRNA modification gtpase trme. Chain:  A, domain 2       1xzpA03 A:212-378 P-loop containing nucleotide triphosphate hydrolases                                                                                                 1xzpA02 A:118-211,A:379-450                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MMR_HSR1-1xzpA01 A:213-327                                                                                         -----------------------------------------------GTPase_Cys_C-1xzpA02 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
                 1xzp A  -5 SSVDKLMDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKMDLTSAEAVRDLIEAKSETSLKLSLRNLKGGLRDFVDSLRRELIEVLAEIRVELDYPDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMVIVGKPNVGKSTLLNRLLNEDRAIVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEKINEEEIKNKLGTDRHMVKISALKGEGLEKLEESIYRETQEIFERGSDSLITNLRQKQLLENVKGHLEDAIKSLKEGMPVDMASIDLERALNLLDEVTGRSFREDLLDTIFSNFCVGK 450
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with MNME_THEMA | Q9WYA4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:131
                                         1                                                                                                                     
                                     -   |     7        17        27        37        47        57        67        77        87        97       107       117 
           MNME_THEMA     - -------------MDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKM 118
               SCOP domains -------------d1xzpb1 B:1-117 TrmE formyl-THF-binding domain                                                                       - SCOP domains
               CATH domains 1xzpB00 B:-12-118 Probable tRNA modification gtpase trme; domain 1                                                                  CATH domains
           Pfam domains (1) ---------------TrmE_N-1xzpB01 B:3-117                                                                                             - Pfam domains (1)
           Pfam domains (2) ---------------TrmE_N-1xzpB02 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
                 1xzp B -12 HWGSPNSSSVDKLMDTIVAVATPPGKGAIAILRLSGPDSWKIVQKHLRTRSKIVPRKAIHGWIHENGEDVDEVVVVFYKSPKSYTGEDMVEVMCHGGPLVVKKLLDLFLKSGARMAEPGEFTKRAFLNGKM 118
                                    -3         7        17        27        37        47        57        67        77        87        97       107       117

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: FBD (14)

Family: TrmE_N (2)

Thermotoga maritima (2)

1a	TrmE_N-1xzpB01	B:3-117
1b	TrmE_N-1xzpB02	B:3-117

Clan: P-loop_NTPase (1112)

Family: MMR_HSR1 (17)

Thermotoga maritima (5)

MMR_HSR1-1xzpA01

A:213-327

Clan: no clan defined [family: GTPase_Cys_C] (2)

Family: GTPase_Cys_C (2)

Thermotoga maritima (2)

GTPase_Cys_C-1xzpA02

A:375-447

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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	1xzp
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	MNME_THEMA \| Q9WYA4	:	1xzq

1xzq	GTP-BINDING PROTEIN TRME COMPLEXED WITH 5-FORMYL-THF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

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