2VGN - JenaLib

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Title :   STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.

Authors :   M. Graille, M. Chaillet, H. Van Tilbeurgh

Date :   14 Nov 07 (Deposition) - 22 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Translation Termination Factor, Protein Biosynthesis, Translation Regulation, Cell Division, Mrna Degradation, Nucleotide Binding, Mitosis, Meiosis, Cytoplasm, Cell Cycle, No-Go Decay (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Graille, M. Chaillet, H. Van Tilbeurgh
Structure Of Yeast Dom34: A Protein Related To Translation Termination Factor Erf1 And Involved In No-Go Decay.
J. Biol. Chem. V. 283 7145 2008
PubMed-ID: 18180287 | Reference-DOI: 10.1074/JBC.M708224200

Molecule 1 - DOM34
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	SEMET SUBSTITUTED PROTEIN
	Strain	:	S288C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 21)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:40 , VAL B:88 , THR B:89	BINDING SITE FOR RESIDUE GOL B1382
2	AC2	SOFTWARE	PHE B:125 , LYS B:128 , MSE B:339 , GLU B:343 , ALA B:349 , LEU B:350 , VAL B:351	BINDING SITE FOR RESIDUE GOL B1383
3	AC3	SOFTWARE	LYS B:8 , LYS B:293 , ASP B:295 , LYS B:297	BINDING SITE FOR RESIDUE PO4 B1384

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

(no "Cis Peptide Bond" information available for 2VGN)

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

(no "PROSITE Motif" information available for 2VGN)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL001W	1	YNL001W.1	XIV:627459-628619	1161	DOM34_YEAST	1-386	386	2	A:1-382 (gaps) B:1-381 (gaps)	382 381

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:360
 aligned with DOM34_YEAST | P33309 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:382
                                    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  
          DOM34_YEAST     1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKFTSKLDEAGKKKSTDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDED 382
               SCOP domains d2vgna1 A:1-135 Dom34                                                                                                                  d2vgna2 A:136-277 Dom34                                                                                                                       d2vgna3 A:278-382 Dom34                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee..hhhhhhhhhh......eeeeee..-------------..eeeeeeeeeeeee....eeeeeeee................eeeee......eeeee...hhhhhhhhhhh........eeeeeee..eeeeeee....eeeeeeee.---------.....hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhh..eeeeeee.hhhhh.hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh..eeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-382 (gaps) UniProt: 1-386 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 2vgn A   1 mKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKF-------------DLVKLKIKVISEDFDmKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFmQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEY---------DVLKFDEKTEKFYKAIYSAmKKDLNFDKLKTIILCSPGFYAKILmDKIFQYAEEEHNKKILDNKGmFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEImVmDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLmDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDED 382
                            |       10        20        30        40      |  -         -|       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  
                            |                                            47            61             76-MSE                                           126-MSE                                     170       180                199-MSE                  224-MSE              245-MSE                              282-MSE                                                  339-MSE                                       
                            1-MSE                                                                                                                                                                                                                                                                                    284-MSE

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with DOM34_YEAST | P33309 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:381
                                    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 
          DOM34_YEAST     1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKFTSKLDEAGKKKSTDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDE 381
               SCOP domains d2vgnb1 B   :1-135 Dom34                                                                                                               d2vgnb2 B:136-277 Dom34                                                                                                                       d2vgnb3 B:278-381 Dom34                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) eRF1_1-2v   gnB05 B:1-136                                                                                                               ----eRF1_2-2vgnB03 B:141-274                                                                                                              --eRF1_3-2vgnB01 B:277-376                                                                            ----- Pfam domains (1)
           Pfam domains (2) eRF1_1-2v   gnB06 B:1-136                                                                                                               ----eRF1_2-2vgnB04 B:141-274                                                                                                              --eRF1_3-2vgnB02 B:277-376                                                                            ----- Pfam domains (2)
         Sec.struct. author .eeeeeee.---...eeeeee..hhhhhhhhhh......eeeeee..------------...eeeeeeeeeeeee....eeeeeeee................eeeee......eeeee...hhhhhhhhhhhhhhhhh..eeeeee...eeeeeee....eeeeeeee.----------....hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-381 (gaps) UniProt: 1-386 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2vgn B   1 mKVISLKKD---KGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKF------------TDLVKLKIKVISEDFDmKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFmQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEY----------VLKFDEKTEKFYKAIYSAmKKDLNFDKLKTIILCSPGFYAKILmDKIFQYAEEEHNKKILDNKGmFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEImVmDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLmDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDE 381
                            |       |-  |     20        30        40      |  -        60        70     |  80        90       100       110       120     | 130       140       150       160       170         -|      190       200       210       220   |   230       240    |  250       260       270       280 | |   290       300       310       320       330       340       350       360       370       380 
                            1-MSE   9  13                                47           60              76-MSE                                           126-MSE                                     170        181               199-MSE                  224-MSE              245-MSE                              282-MSE                                                  339-MSE                                      
                                                                                                                                                                                                                                                                                                                     284-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 "CATH Domain" information available for 2VGN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DOM34_YEAST | P33309)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0071025	RNA surveillance	The set of processes involved in identifying and degrading defective or aberrant RNAs.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0070651	nonfunctional rRNA decay	An rRNA catabolic process that results in the targeted detection and degradation of aberrant rRNAs contained within translationally defective ribosomes, thereby acting as a quality-control system.
	GO:0070966	nuclear-transcribed mRNA catabolic process, no-go decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
	GO:0070481	nuclear-transcribed mRNA catabolic process, non-stop decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	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:0006417	regulation of translation	Any process that modulates 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:0032790	ribosome disassembly	The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
	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.
cellular component
	GO:1990533	Dom34-Hbs1 complex	A protein complex consisting of one subunit known as Dom34 or Pelota that has similarity to translation termination factor eRF1, and another subunit, Hbs1, that is a GTPase with similarity to translation termination factor eRF3. The Dom34-Hbs1 complex has a role in cotranslational mRNA quality control by promoting ribosomal subunit dissociation and peptidyl-tRNA release when translation is stalled, facilitating no-go decay and nonstop decay.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	DOM34_YEAST \| P33309	:	2vgm 3izq 3j16 5m1j

2vgm	STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 21)

Sites (3, 3)

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