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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF GTP-BOUND LEPA FROM AQUIFEX AEOLICUS

Authors :   M. Kawazoe, C. Takemoto, T. Kaminishi, A. Nishino, R. Nakayama-Ushiko K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, S. Yokoyama, Riken Stru Genomics/Proteomics Initiative (Rsgi)

Date :   20 Apr 07 (Deposition) - 29 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.94

Chains :   Asym./Biol. Unit : A

Keywords :   G Domain, Beta-Barrel, Ferredoxin-Like Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kawazoe, C. Takemoto, T. Kaminishi, A. Nishino, R. Nakayama-Ushikoshi, K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structures Of Gtp-Binding Protein Lepa From Aquifex Aeolicus
To Be Published
PubMed: search

Molecule 1 - GTP-BINDING PROTEIN LEPA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AQ_1725
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:16 , HIS A:17 , GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:164 , ALA A:165 , LYS A:166 , HOH A:716 , HOH A:729	BINDING SITE FOR RESIDUE GTP A 701

(no "SS Bond" information available for 2YWG)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:243	-	Pro A:244

(no "SAP(SNP)/Variant" information available for 2YWG)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	LEPA_AQUAE	44-59	1	A:56-59

(no "Exon" information available for 2YWG)

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:528
 aligned with LEPA_AQUAE | O67618 from UniProtKB/Swiss-Prot  Length:600

    Alignment length:551
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           LEPA_AQUAE     1 MEQKNVRNFCIIAHVDHGKSTLADRLLEYTGAISEREKREQLLDTLDVERERGITVKMQAVRMFYKAKDGNTYKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDLPSADVDRVKKQIEEVLGLDPEEAILASAKEGIGIEEILEAIVNRIPPPKGDPQKPLKALIFDSYYDPYRGAVAFVRIFDGEVKPGDKIMLMSTGKEYEVTEVGAQTPKMTKFDKLSAGDVGYIAASIKDVRDIRIGDTITHAKNPTKEPVPGFQPAKPMVYAGIYPAEDTTYEELRDALEKYAINDAAIVYEPESSPALGMGFRVGFLGLLHMEIVQERLEREYGVKIITTAPNVIYRVKKKFTDEVIEVRNPMDFPDNAGLIEYVEEPFVLVTIITPKEYVGPIIQLCQEKRGIQKNMTYLDPNTVYLEYEMPLSEIIVDFHDKIKSISRGFASYDYEFIGYRPSDLIKLTVLINKKPVDALSFIVHADRAQKFARRVAEKLRETIPRQLFEVHIQVAKGGKVIASERIKPLR 551
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---GTP_EFTU-2ywgA02 A:4-184                                                                                                                                                             ----------------------GTP_EFTU_D2-2ywgA03 A:207-277                                          ----------------------------------------------------------------------------------------------------------------------------EFG_C-2ywgA01 A:402-491                                                                   LepA_C-2ywgA04 A:492-551                                     Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhhhhh-----------------------.....eeeeee.....eeeeeee....hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh......eee......hhhhhhhhhhhhh...........eeeeeeeeee...eeeeeeeeee.ee....eeee.....eee..eeeee...eeee..ee...eeeeeeee..........eeee..................eeeeeee....hhhhhhhhhhhhhhhh...eeeeeee...eeeeeeee.hhhhhhhhhhhhhh.....eee...ee.eeeee......eee.hhhhh..hhh.eeeeeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeehhhhh.hhhhhhhhh.....eeeeeeeeeee..eeeeeeee....hhhhheeee..hhhhhhhhhhhhhhhhh......eeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywg A   1 mEQKNVRNFCIIAHVDHGKSTLADRLLEYTGA-----------------------VKmQAVRmFYKAKDGNTYKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDLPSADVDRVKKQIEEVLGLDPEEAILASAKEGIGIEEILEAIVNRIPPPKGDPQKPLKALIFDSYYDPYRGAVAFVRIFDGEVKPGDKImLmSTGKEYEVTEVGAQTPKmTKFDKLSAGDVGYIAASIKDVRDIRIGDTITHAKNPTKEPVPGFQPAKPmVYAGIYPAEDTTYEELRDALEKYAINDAAIVYEPESSPALGmGFRVGFLGLLHmEIVQERLEREYGVKIITTAPNVIYRVKKKFTDEVIEVRNPmDFPDNAGLIEYVEEPFVLVTIITPKEYVGPIIQLCQEKRGIQKNmTYLDPNTVYLEYEmPLSEIIVDFHDKIKSISRGFASYDYEFIGYRPSDLIKLTVLINKKPVDALSFIVHADRAQKFARRVAEKLRETIPRQLFEVHIQVAKGGKVIASERIKPLR 551
                            |       10        20        30 |       -         -     | |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       310       320       330       340       350       360       370       380       390|      400       410       420       430     | 440       450       460       470       480       490       500       510       520       530       540       550 
                            |                             32                      56 |    |                                                                                                                                                                226-MSE             246-MSE                                           296-MSE                                   338-MSE     350-MSE                                  391-MSE                                      436-MSE       450-MSE                                                                                                 
                            1-MSE                                                   58-MSE|                                                                                                                                                                  228-MSE                                                                                                                                                                                                                                                                                                                               
                                                                                         63-MSE

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 '\|'

(no "SCOP Domain" information available for 2YWG)

(no "CATH Domain" information available for 2YWG)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF-G_C (20)

Family: EFG_C (14)

Aquifex aeolicus (3)

EFG_C-2ywgA01

A:402-491

Clan: P-loop_NTPase (1112)

Family: GTP_EFTU (39)

Aquifex aeolicus (3)

GTP_EFTU-2ywgA02

A:4-184

Clan: no clan defined [family: GTP_EFTU_D2] (39)

Family: GTP_EFTU_D2 (39)

Aquifex aeolicus (3)

GTP_EFTU_D2-2ywgA03

A:207-277

Clan: no clan defined [family: LepA_C] (3)

Family: LepA_C (3)

Aquifex aeolicus (3)

LepA_C-2ywgA04

A:492-551

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LEPA_AQUAE | O67618)

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: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:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
	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.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Thr A:243 - Pro A:244	[ RasMol ]

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	2ywg
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UniProtKB/Swiss-Prot
	LEPA_AQUAE \| O67618	:	2ywe 2ywf 2ywh

2ywe
2ywf
2ywh	RELATED ID: AAE001001725.3 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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Pfam Domains (4, 4)

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