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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   METHYLATED FORM OF N-TERMINAL TRANSCRIPTIONAL REGULATOR DOMAIN OF ESCHERICHIA COLI ADA PROTEIN

Authors :   H. Takinowaki, Y. Matsuda, T. Yoshida, Y. Kobayashi, T. Ohkubo

Date :   07 Sep 04 (Deposition) - 13 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (17x)

Keywords :   Zinc Coordination, Helix-Turn-Helix, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Takinowaki, Y. Matsuda, T. Yoshida, Y. Kobayashi, T. Ohkubo
The Solution Structure Of The Methylated Form Of The N-Terminal 16-Kda Domain Of Escherichia Coli Ada Protein
Protein Sci. V. 15 487 2006
PubMed-ID: 16452614 | Reference-DOI: 10.1110/PS.051786306
(for further references see the PDB file header)

Molecule 1 - ADA REGULATORY PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K12
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	K12
	Expression System Taxid	:	83333
	Expression System Vector Type	:	PLASMID
	Fragment	:	METHYLATED N-TERMINAL 16 KDA DOMAIN
	Gene	:	ADA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	REGULATORY PROTEIN OF ADAPTATIVE RESPONSE


NMR Structure (17x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

No.	Name	Count	Type	Full Name
1	SMC	1	Mod. Amino Acid	S-METHYLCYSTEINE
2	ZN	1	Ligand/Ion	ZINC ION

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SMC A:38 , CYS A:42 , CYS A:69 , LYS A:70 , CYS A:72	BINDING SITE FOR RESIDUE ZN A 200

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

(no "Cis Peptide Bond" information available for 1WPK)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ADA_ECOLI_001 *	E	75	D	ADA_ECOLI	---	---	A	E	75	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARAC_FAMILY_2	PS01124	Bacterial regulatory proteins, araC family DNA-binding domain profile.	ADA_ECOLI	85-183	1	A:85-146
2	HTH_ARAC_FAMILY_1	PS00041	Bacterial regulatory proteins, araC family signature.	ADA_ECOLI	86-128 136-177	2	A:86-128 A:136-146

(no "Exon" information available for 1WPK)

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:146
 aligned with ADA_ECOLI | P06134 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            ADA_ECOLI     1 MKKATCLTDDQRWQSVLARDPNADGEFVFAVRTTGIFCRPSCRARHALRENVSFYANASEALAAGFRPCKRCQPEKANAQQHRLDKITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLRESLAK 146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------1wpkA01 A:8-79 DNA Methylphosphotriester Repair Domain                  1wpkA02 A:80-146 Homeodomain-like                                   CATH domains
           Pfam domains (1) ---------Ada_Zn_binding-1wpkA03 A:10-75                                    ----------------------------------------------------------------HTH_Ara Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------HTH_Ara Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhh........eeee....eee.............eeee.hhhhhhhhhheee............hhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------D----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------HTH_ARAC_FAMILY_2  PDB: A:85-146 UniProt: 85-183               PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------HTH_ARAC_FAMILY_1  PDB: A:86-128           -------HTH_ARAC_FA PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wpk A   1 MKKATCLTDDQRWQSVLARDPNADGEFVFAVRTTGIFcRPSCRARHALRENVSFYANASEALAAGFRPCKRCQPEKANAQQHRLDKITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLRESLAK 146
                                    10        20        30       |40        50        60        70        80        90       100       110       120       130       140      
                                                                38-SMC

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 "SCOP Domain" information available for 1WPK)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_AraC (3)

Escherichia coli (strain K12) (3)

1a	HTH_AraC-1wpkA01	A:140-146
1b	HTH_AraC-1wpkA02	A:140-146

Clan: no clan defined [family: Ada_Zn_binding] (3)

Family: Ada_Zn_binding (3)

Escherichia coli (strain K12) (3)

Ada_Zn_binding-1wpkA03

A:10-75

NMR Structure(hide GO term definitions)

Chain A (ADA_ECOLI | P06134)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003908	methylated-DNA-[protein]-cysteine S-methyltransferase activity	Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006307	DNA dealkylation involved in DNA repair	The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
	GO:0080111	DNA demethylation	The removal of a methyl group from one or more nucleotides within an DNA molecule.
	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:0006974	cellular response to DNA damage stimulus	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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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.

NMR Structure
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	1wpk
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UniProtKB/Swiss-Prot
	ADA_ECOLI \| P06134	:	1adn 1eyf 1sfe 1u8b 1zgw

6054	1H, 15N AND 13C RESONANCE ASSIGNMENTS OF THIS PROTEIN.
1adn	SOLUTION STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA.
1eyf	REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF E. COLI ADA.

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (19, 19)

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