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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MRNA DECAPPING ENZYME (DCPS) FROM MUS MUSCULUS AT 1.83 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   10 Aug 04 (Deposition) - 24 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

Chains :   Asym./Biol. Unit : A,B

Keywords :   16740816, Mrna Decapping Enzyme (Dcps), Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. W. Han, R. Schwarzenbacher, D. Mcmullan, P. Abdubek, E. Ambing, H. Axelrod, T. Biorac, J. M. Canaves, H. J. Chiu, X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, J. Haugen, M. Hornsby, L. Jaroszewski, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, T. M. Mcphillips, M. D. Miller, K. Moy, E. Nigoghossian, J. Paulsen, K. Quijano, R. Reyes, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of An Apo Mrna Decapping Enzyme (Dcps) From Mouse At 1. 83 A Resolution.
Proteins V. 60 797 2005
PubMed-ID: 16001405 | Reference-DOI: 10.1002/PROT.20467
(for further references see the PDB file header)

Molecule 1 - MRNA DECAPPING ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCPS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	HISTIDINE TRIAD PROTEIN MEMBER 5

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:45 , ARG B:47 , LYS B:66 , VAL B:67 , GLU B:69 , GLU B:235 , HOH B:565	BINDING SITE FOR RESIDUE EDO B 339
2	AC2	SOFTWARE	PHE A:190 , GLU A:246 , GLU A:249 , ALA A:250 , LYS A:253 , HOH A:568	BINDING SITE FOR RESIDUE EDO A 339
3	AC3	SOFTWARE	GLY A:76	BINDING SITE FOR RESIDUE EDO A 340
4	AC4	SOFTWARE	GLN A:299 , HOH A:630 , ASN B:303 , HIS B:310 , ARG B:314 , THR B:315 , LEU B:316 , HOH B:701	BINDING SITE FOR RESIDUE EDO A 341
5	AC5	SOFTWARE	ASN A:303 , HIS A:310 , ARG A:314 , THR A:315 , LEU A:316 , HOH A:373 , HOH A:497 , GLN B:299	BINDING SITE FOR RESIDUE EDO A 342
6	AC6	SOFTWARE	HOH A:444 , PRO B:119 , PRO B:120 , ARG B:121 , SER B:124	BINDING SITE FOR RESIDUE EDO B 340

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:132	-	Pro A:133
2	Tyr A:268	-	Leu A:269
3	Tyr B:132	-	Pro B:133
4	Tyr B:268	-	Leu B:269

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_1	PS00892	HIT domain signature.	DCPS_MOUSE	263-281	2	A:263-281 B:263-281

(no "Exon" information available for 1VLR)

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:290
 aligned with DCPS_MOUSE | Q9DAR7 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:300
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
           DCPS_MOUSE    38 PVRLPFSGFRVQKVLRESARDKIIFLHGKVNEDSGDTHGEDAVVILEKTPFQVEHVAQLLTGSPELKLQFSNDIYSTYNLFPPRHLSDIKTTVVYPATEKHLQKYMRQDLRLIRETGDDYRTITLPYLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILREGQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENLECDPKHYQQRTLTFALRTDDPLLQLLQKAQQER 337
               SCOP domains -d1vlra2 A:39-145 mRNA decapping       enzyme DcpS N-terminal domain                                        d1vlra1 A:146-337 mRNA decapping enz    yme DcpS C-terminal domain                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeee....eeeeeeee..------.eeeeeeeee...hhhhhhhhhh...eeeeeee...eeeeeee.hhhhhheeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhh.----....eee......eeeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIT_1              -------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vlr A  38 PVRLPFSGFRVQKVLRESARDKIIFLHGKVNE------GEDAVVILEKTPFQVEHVAQLLTGSPELKLQFSNDIYSTYNLFPPRHLSDIKTTVVYPATEKHLQKYMRQDLRLIRETGDDYRTITLPYLESQSLSIQWVYNILDK----DRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILREGQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENLECDPKHYQQRTLTFALRTDDPLLQLLQKAQQER 337
                                    47        57        67 |      77        87        97       107       117       127       137       147       157       167       177   |   187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
                                                          69     76                                                                                                      181  186

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with DCPS_MOUSE | Q9DAR7 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:299
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           DCPS_MOUSE    39 VRLPFSGFRVQKVLRESARDKIIFLHGKVNEDSGDTHGEDAVVILEKTPFQVEHVAQLLTGSPELKLQFSNDIYSTYNLFPPRHLSDIKTTVVYPATEKHLQKYMRQDLRLIRETGDDYRTITLPYLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILREGQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENLECDPKHYQQRTLTFALRTDDPLLQLLQKAQQER 337
               SCOP domains d1vlrb2 B:39-145 mRNA decapping        enzyme DcpS N-terminal domain                                       d1vlrb1 B:146-337 mRNA decapping enzyme DcpS C-terminal domain                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -DcpS-1vlrB03 B:40-145                                                                                     ---------------------------DcpS_C-1vlrB01 B:173-293                                                                                                 -------------------------------------------- Pfam domains (1)
           Pfam domains (2) -DcpS-1vlrB04 B:40-145                                                                                     ---------------------------DcpS_C-1vlrB02 B:173-293                                                                                                 -------------------------------------------- Pfam domains (2)
         Sec.struct. author ........eeeeeeeee....eeeeeee...-------.eeeeeeee...hhhhhhhhhh...eeeeeee...eeeeeee.hhhhh.eeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhh....hhhhhhhhh...hhhhh.eee......eeeee.......hhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIT_1              -------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vlr B  39 VRLPFSGFRVQKVLRESARDKIIFLHGKVNE-------EDAVVILEKTPFQVEHVAQLLTGSPELKLQFSNDIYSTYNLFPPRHLSDIKTTVVYPATEKHLQKYMRQDLRLIRETGDDYRTITLPYLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILREGQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENLECDPKHYQQRTLTFALRTDDPLLQLLQKAQQER 337
                                    48        58        68|       78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
                                                         69      77

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 1VLR)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HIT (23)

Family: DcpS_C (4)

Mus musculus (Mouse) (1)

1a	DcpS_C-1vlrB01	B:173-293
1b	DcpS_C-1vlrB02	B:173-293

Clan: no clan defined [family: DcpS] (4)

Family: DcpS (4)

Mus musculus (Mouse) (1)

2a	DcpS-1vlrB03	B:40-145
2b	DcpS-1vlrB04	B:40-145

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DCPS_MOUSE | Q9DAR7)

molecular function
	GO:0000340	RNA 7-methylguanosine cap binding	Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0050072	m7G(5')pppN diphosphatase activity	Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0036245	cellular response to menadione	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position.
	GO:0000290	deadenylation-dependent decapping of nuclear-transcribed mRNA	Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
	GO:0045292	mRNA cis splicing, via spliceosome	The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0043069	negative regulation of programmed cell death	Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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		Tyr A:268 - Leu A:269	[ RasMol ]
		Tyr B:132 - Pro B:133	[ RasMol ]
		Tyr B:268 - Leu B:269	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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