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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE R3H DOMAIN FROM HUMAN SMUBP-2 IN COMPLEX WITH 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

Authors :   K. Jaudzems, D. Zhulenkovs, G. Otting, E. Liepinsh

Date :   12 Apr 12 (Deposition) - 24 Oct 12 (Release) - 24 Oct 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Dna Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Jaudzems, X. Jia, H. Yagi, D. Zhulenkovs, B. Graham, G. Otting, E. Liepinsh
Structural Basis For 5'-End-Specific Recognition Of Single-Stranded Dna By The R3H Domain From Human Smubp-2
J. Mol. Biol. V. 12 760 2012
PubMed-ID: 22999958 | Reference-DOI: 10.1016/J.JMB.2012.09.010

Molecule 1 - DNA-BINDING PROTEIN SMUBP-2
	Chains	:	A
	EC Number	:	3.6.4.12, 3.6.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector	:	PQE60
	Fragment	:	R3H DOMAIN RESIDUES 711-786
	Gene	:	IGHMBP2, SMBP2, SMUBP-2, SMUBP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ATP-DEPENDENT HELICASE IGHMBP2, GLIAL FACTOR 1, GF-1, IMMUNOGLOBULIN MU-BINDING PROTEIN 2

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	DGP	1	Ligand/Ion	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

NMR Structure * (1, 1)

No.	Name	Count	Type	Full Name
1	DGP	1	Ligand/Ion	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:752 , ARG A:755 , LEU A:756 , HIS A:759 , GLU A:763 , HIS A:769 , SER A:771 , ARG A:778	BINDING SITE FOR RESIDUE DGP A 801

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	R3H	PS51061	R3H domain profile.	SMBP2_HUMAN	723-786	1	A:723-786

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	R3H	PS51061	R3H domain profile.	SMBP2_HUMAN	723-786	1	A:723-786

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000255078	1	ENSE00001200470	chr11:68671319-68671506	188	SMBP2_HUMAN	1-29	29	0	-	-
1.2	ENST00000255078	2	ENSE00001064263	chr11:68673537-68673706	170	SMBP2_HUMAN	29-86	58	0	-	-
1.3	ENST00000255078	3	ENSE00001117306	chr11:68675613-68675805	193	SMBP2_HUMAN	86-150	65	0	-	-
1.4	ENST00000255078	4	ENSE00001117303	chr11:68676002-68676099	98	SMBP2_HUMAN	150-183	34	0	-	-
1.5	ENST00000255078	5	ENSE00001200445	chr11:68678908-68679071	164	SMBP2_HUMAN	183-237	55	0	-	-
1.6	ENST00000255078	6	ENSE00000737364	chr11:68682291-68682491	201	SMBP2_HUMAN	238-304	67	0	-	-
1.7	ENST00000255078	7	ENSE00001117311	chr11:68685204-68685351	148	SMBP2_HUMAN	305-354	50	0	-	-
1.8	ENST00000255078	8	ENSE00001117308	chr11:68696651-68696825	175	SMBP2_HUMAN	354-412	59	0	-	-
1.9	ENST00000255078	9	ENSE00001200438	chr11:68700767-68700949	183	SMBP2_HUMAN	412-473	62	0	-	-
1.10	ENST00000255078	10	ENSE00001200433	chr11:68701263-68701381	119	SMBP2_HUMAN	473-513	41	0	-	-
1.11	ENST00000255078	11	ENSE00001200427	chr11:68701932-68702026	95	SMBP2_HUMAN	513-544	32	0	-	-
1.12	ENST00000255078	12	ENSE00001200421	chr11:68702767-68702890	124	SMBP2_HUMAN	545-586	42	0	-	-
1.13	ENST00000255078	13	ENSE00001165813	chr11:68703705-68704559	855	SMBP2_HUMAN	586-871	286	1	A:717-786	70
1.14	ENST00000255078	14	ENSE00001200411	chr11:68705650-68705822	173	SMBP2_HUMAN	871-928	58	0	-	-
1.15	ENST00000255078	15	ENSE00001311607	chr11:68707002-68708069	1068	SMBP2_HUMAN	929-993	65	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:70
 aligned with SMBP2_HUMAN | P38935 from UniProtKB/Swiss-Prot  Length:993

    Alignment length:70
                                   726       736       746       756       766       776       786
          SMBP2_HUMAN   717 PEGVESQDGVDHFRAMIVEFMASKKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKRA 786
               SCOP domains d2lrra_ A: automated matches                                           SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------R3H  PDB: A:723-786 UniProt: 723-786                             PROSITE
               Transcript 1 Exon 1.13  PDB: A:717-786 UniProt: 586-871 [INCOMPLETE]                Transcript 1
                 2lrr A 717 PEGVESQDGVDHFRAMIVEFMASKKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKRA 786
                                   726       736       746       756       766       776       786

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: IF3-like (127)

Superfamily: R3H domain (4)

Family: R3H domain (4)

Protein domain: automated matches (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2lrra_

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

(no "Pfam Domain" information available for 2LRR)

NMR Structure(hide GO term definitions)

Chain A (SMBP2_HUMAN | P38935)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0043141	ATP-dependent 5'-3' DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 5' to 3'.
	GO:0032575	ATP-dependent 5'-3' RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix in the direction 5' to 3'.
	GO:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003678	DNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008186	RNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	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.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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:0032797	SMN complex	A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

NMR Structure
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	2lrr
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	SMBP2_HUMAN \| P38935
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	3.6.4.12
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	SMBP2_HUMAN \| P38935	:	1msz 4b3f 4b3g

1msz	STRUCTURE OF LIGAND FREE FORM RELATED ID: 18391 RELATED DB: BMRB

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Ligands, Modified Residues, Ions (1, 1)

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