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Description

Title :   HUMAN DEAD-BOX RNA HELICASE DDX10, DEAD DOMAIN IN COMPLEX WITH ADP

Authors :   T. Karlberg, L. Lehtio, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Co L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, B. M. Hal M. Hammarstrom, I. Johansson, A. Kallas, T. Kotenyova, M. Moche, P. No T. Nyman, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Tho S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone, Structural Ge Consortium (Sgc)

Date :   19 Apr 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Rna, Helicase, Dead, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
PubMed-ID: 20941364 | Reference-DOI: 10.1371/JOURNAL.PONE.0012791

Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX10
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3) GOLD PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DEAD DOMAIN
	Gene	:	DDX10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEAD BOX PROTEIN 10

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 6)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	EOH	4	Ligand/Ion	ETHANOL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:223 , ADP A:300 , HOH A:404 , HOH A:405 , HOH A:406 , HOH A:469	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	SER A:45 , MET A:46 , GLN A:47 , ARG A:50 , PHE A:71 , TYR A:89 , LEU A:91 , GLN A:96 , THR A:115 , GLY A:116 , SER A:117 , GLY A:118 , LYS A:119 , THR A:120 , GLU A:223 , MG A:301 , HOH A:404 , HOH A:406 , HOH A:410 , HOH A:415 , HOH A:448 , HOH A:469	BINDING SITE FOR RESIDUE ADP A 300
3	AC3	SOFTWARE	LEU A:153	BINDING SITE FOR RESIDUE EOH A 400
4	AC4	SOFTWARE	GLN A:98 , GLN A:256 , LYS A:258 , LYS A:261 , HOH A:417	BINDING SITE FOR RESIDUE EOH A 401
5	AC5	SOFTWARE	ALA A:112 , ALA A:254 , TRP A:275 , VAL A:276 , HIS A:277	BINDING SITE FOR RESIDUE EOH A 402
6	AC6	SOFTWARE	ALA A:233 , ASN A:237 , LEU A:263 , LEU A:266	BINDING SITE FOR RESIDUE EOH A 403

SS Bonds (0, 0)

(no "SS Bond" information available for 2PL3)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2PL3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2PL3)

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DDX10_HUMAN	69-97	1	A:69-97
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX10_HUMAN	220-228	1	A:220-228

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000322536	1a	ENSE00002146160	chr11:108535752-108536066	315	DDX10_HUMAN	1-62	62	1	A:45-62	18
1.2	ENST00000322536	2	ENSE00001005166	chr11:108544194-108544254	61	DDX10_HUMAN	63-83	21	1	A:63-83	21
1.3a	ENST00000322536	3a	ENSE00001005161	chr11:108546323-108546453	131	DDX10_HUMAN	83-126	44	1	A:83-126	44
1.4	ENST00000322536	4	ENSE00001224552	chr11:108547812-108547970	159	DDX10_HUMAN	127-179	53	1	A:127-178	52
1.5	ENST00000322536	5	ENSE00001309598	chr11:108549042-108549162	121	DDX10_HUMAN	180-220	41	1	A:181-220	40
1.6a	ENST00000322536	6a	ENSE00001291421	chr11:108550098-108550287	190	DDX10_HUMAN	220-283	64	1	A:220-278	59
1.7	ENST00000322536	7	ENSE00001307885	chr11:108559663-108559789	127	DDX10_HUMAN	283-325	43	0	-	-
1.8	ENST00000322536	8	ENSE00001317728	chr11:108562603-108562765	163	DDX10_HUMAN	326-380	55	0	-	-
1.9	ENST00000322536	9	ENSE00001005159	chr11:108564243-108564327	85	DDX10_HUMAN	380-408	29	0	-	-
1.10	ENST00000322536	10	ENSE00001224211	chr11:108577466-108577564	99	DDX10_HUMAN	408-441	34	0	-	-
1.11	ENST00000322536	11	ENSE00001295492	chr11:108586606-108586693	88	DDX10_HUMAN	441-470	30	0	-	-
1.12	ENST00000322536	12	ENSE00001325848	chr11:108590524-108590612	89	DDX10_HUMAN	471-500	30	0	-	-
1.13	ENST00000322536	13	ENSE00001224190	chr11:108593724-108594189	466	DDX10_HUMAN	500-655	156	0	-	-
1.16b	ENST00000322536	16b	ENSE00001102046	chr11:108709173-108709292	120	DDX10_HUMAN	656-695	40	0	-	-
1.17	ENST00000322536	17	ENSE00001102034	chr11:108712042-108712203	162	DDX10_HUMAN	696-749	54	0	-	-
1.18	ENST00000322536	18	ENSE00001102064	chr11:108722880-108722936	57	DDX10_HUMAN	750-768	19	0	-	-
1.21b	ENST00000322536	21b	ENSE00001224158	chr11:108788600-108788745	146	DDX10_HUMAN	769-817	49	0	-	-
1.23d	ENST00000322536	23d	ENSE00002169559	chr11:108810973-108811657	685	DDX10_HUMAN	817-875	59	0	-	-

Sequences/Alignments

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:232
 aligned with DDX10_HUMAN | Q13206 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:234
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274    
          DDX10_HUMAN    45 EWQVERESISRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE 278
               SCOP domains d2pl3a_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2pl3A00 A:45-278 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------DEAD-2pl3A01 A:93-263                                                                                                                                                      --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhh.hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..hhhhh..eeee..hhhhhhhhhhhhhhhh......eeee...--hhhhhhhhh...eeeehhhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhh.....eeeeee...hhhhhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------Q_MOTIF  PDB: A:69-97        --------------------------------------------------------------------------------------------------------------------------DEAD_ATP_-------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a         Exon 1.2  PDB: A:63-8-------------------------------------------Exon 1.4  PDB: A:127-178 UniProt: 127-179            Exon 1.5  PDB: A:181-220 UniProt: 180-220---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3a  PDB: A:83-126 UniProt: 83-126    ---------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:220-278 UniProt: 220-283 [INCOMPLETE]     Transcript 1 (2)
                 2pl3 A  45 SMQVERESISRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGG--LKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE 278
                                    54        64        74        84        94       104       114       124       134       144       154       164       174   |  |184       194       204       214       224       234       244       254       264       274    
                                                                                                                                                               178  |                                                                                                 
                                                                                                                                                                  181

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Human (Homo sapiens) [TaxId: 9606] (86)

d2pl3a_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

2pl3A00

A:45-278

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DEAD (41)

Homo sapiens (Human) (12)

DEAD-2pl3A01

A:93-263

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DDX10_HUMAN | Q13206)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.

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	2pl3
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (6, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

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Related Entries

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