1U2R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ADP-RIBOSYLATED RIBOSOMAL TRANSLOCASE FROM SACCHAROMYCES CEREVISIAE

Authors :   R. Jorgensen, S. P. Yates, J. Nilsson, G. A. Prentice, D. J. Teal, A. R. Merrill, G. R. Andersen

Date :   20 Jul 04 (Deposition) - 14 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A

Keywords :   Adp-Ribosylation, Eukaryotic Elongation Factor 2, Diphthamide, Gdp, Sordarin, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Jorgensen, S. P. Yates, D. J. Teal, J. Nilsson, G. A. Prentice, A. R. Merrill, G. R. Andersen
Crystal Structure Of Adp-Ribosylated Ribosomal Translocase From Saccharomyces Cerevisiae
J. Biol. Chem. V. 279 45919 2004
PubMed-ID: 15316019 | Reference-DOI: 10.1074/JBC.M406218200
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR 2
	Chains	:	A
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EF-2, ADPR-EF2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	DDE	1	Mod. Amino Acid	{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	SO1	1	Ligand/Ion	[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:33 , GDP A:1920	BINDING SITE FOR RESIDUE MG A 843
2	AC2	SOFTWARE	VAL A:306 , HIS A:694 , ASP A:696 , ILE A:698 , DDE A:699	BINDING SITE FOR RESIDUE APR A 1699
3	AC3	SOFTWARE	GLN A:490 , LEU A:519 , TYR A:521 , SER A:523 , GLU A:524 , VAL A:561 , ALA A:562 , PRO A:727 , PHE A:729 , MET A:796 , VAL A:797 , PHE A:798 , TRP A:801 , HOH A:1921 , HOH A:1940 , HOH A:1951	BINDING SITE FOR RESIDUE SO1 A 1700
4	AC4	SOFTWARE	HIS A:27 , ASP A:29 , HIS A:30 , GLY A:31 , LYS A:32 , SER A:33 , THR A:34 , ASN A:158 , LYS A:159 , ASP A:161 , ARG A:162 , SER A:213 , GLY A:214 , LEU A:215 , MG A:843 , HOH A:1939 , HOH A:1988 , HOH A:2031 , HOH A:2035	BINDING SITE FOR RESIDUE GDP A 1920

(no "SS Bond" information available for 1U2R)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:637	-	Pro A:638

(no "SAP(SNP)/Variant" information available for 1U2R)

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.	EF2_YEAST	58-73	1	A:67-73

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	YOR133W	2	YOR133W.1	XV:575099-577627	2529	EF2_YEAST	1-842	842	1	A:3-842 (gaps)	840

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:819
 aligned with EF2_YEAST | P32324 from UniProtKB/Swiss-Prot  Length:842

    Alignment length:840
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842
            EF2_YEAST     3 AFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
               SCOP domains d1u2ra2 A:3-343 Elongation factor 2 (eEF-2), N                  -terminal (G) domain                                                                                                                                                                                                                                                                 d1u2ra1 A:344-481 Elongation factor 2 (eEF-2), domain II                                                                                  d1u2ra4 A:482-560 Elongation factor 2 (eEF-2)                                  d1u2ra3 A:561-725 Elongation factor 2 (eEF-2), domain IV                                                                                                             d1u2ra5 A:726-842 Elongation facto   r 2 (eEF-2)                                                                      SCOP domains
               CATH domains 1u2rA01 A:3-48,A:74-221,A:329-344                               1u2rA021u2rA01 A:3-48,A:74-221,A:329-344 P-loop containing nucleotide triphosphate hydrolases                                                              1u2rA03 A:222-328 Yeast translation eEF2 (G' domain)                                                       1u2rA01         1u2rA02 A:67-73,A:345-485 Translation factors                                                                                                1u2rA04 A:486-561 Elongation Factor G (Translational Gtpase), domain 3      1u2rA05 1u2rA06 A:570-721,A:829-842  [code=3.30.230.10, no name defined]                                                                                        1u2rA05 A:562-569,A:722-828  [code=3.3   0.70.240, no name defined]                                        1u2rA06        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhh....------------------.......eeeeeee.hhhhhhhh.......eeeeeee........hhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeee....eeeehhhhhhhhhhhhh.hhhhhhhhh....eee....eee............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhh.......eeeeeeeee......eeeeeeeee.eee...eeeee...........eeeee..eeeeee..eeeee.eee...eeeee.........eeee..................eeeeeee.hhhhhhhhhhhhhhhhhhh...eeee.....eeeee.hhhhhhhhhhhhhhh.....eeee......eeee.......eeee......eeeeeeee.hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhheeee.......eeeee......hhhhhhhhhhhhhhhhhhh......ee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeehhhhhhhhhhhhhhh..eeeeee.---...eeeeeeee.hhh.hhhhhhhhhh.......eeeeeeee.........hhhhhhhhhhhhhh.......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:3-842 (gaps) UniProt: 1-842 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 1u2r A   3 AFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISA------------------GITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIhRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQ---TPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
                                    12        22        32        42     |   -         -    |   72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692      |702       712       722       732       742       752      |  -|      772       782       792       802       812       822       832       842
                                                                        48                 67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     699-DDE                                                     759 763

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 "Pfam Domain" information available for 1U2R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (EF2_YEAST | P32324)

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: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).
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:1990145	maintenance of translational fidelity	Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.
	GO:0017183	peptidyl-diphthamide biosynthetic process from peptidyl-histidine	The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.
	GO:0045901	positive regulation of translational elongation	Any process that activates or increases the frequency, rate or extent of translational elongation.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:637 - Pro A:638	[ RasMol ]

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	1u2r
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1n0u	ELONGATION FACTOR 2 FROM YEAST IN COMPLEX WITH SORDARIN
1n0v	ELONGATION FACTOR 2 FROM YEAST

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 5)

CATH Domains (6, 6)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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