1L5Z - JenaLib

Title :   CRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD

Authors :   S. Park, M. Meyer, A. D. Jones, H. P. Yennawar, N. H. Yennawar, B. T. Nixon

Date :   08 Mar 02 (Deposition) - 23 Oct 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (4x)

Keywords :   Two Component Receiver Domain, Sigma 54, Regulator Of Aaa+ Atpase, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Park, M. Meyer, A. D. Jones, H. P. Yennawar, N. H. Yennawar, B. T. Nixo
Two-Component Signaling In The Aaa + Atpase Dctd: Binding Mg2+ And Bef3- Selects Between Alternate Dimeric States Of The Receiver Domain
Faseb J. V. 16 1964 2002
PubMed-ID: 12368235
(for further references see the PDB file header)

Compounds

Molecule 1 - C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT143E121K
	Expression System Strain	:	BL21/DE3/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RECEIVER DOMAIN, RESIDUES 2-143
	Gene	:	DCTD
	Mutation	:	YES
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	382
	Synonym	:	DCTDNL

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:14 , ARG A:17 , HOH A:574	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	ARG A:57 , GLY A:84 , HIS A:85 , GLY A:86 , ASP A:87	BINDING SITE FOR RESIDUE GOL A 501
3	AC3	SOFTWARE	GLN A:22 , ARG A:68 , GLN A:93 , ALA A:94 , ASP A:97	BINDING SITE FOR RESIDUE GOL A 502
4	AC4	SOFTWARE	ILE A:95 , ASP A:101 , ARG A:111 , GLN A:114 , SER A:115 , ARG A:118 , HOH A:559	BINDING SITE FOR RESIDUE GOL A 503
5	AC5	SOFTWARE	HIS A:85 , ILE A:88 , PRO A:89 , ARG A:111 , HOH A:532	BINDING SITE FOR RESIDUE GOL A 504

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	DCTD_RHIME	6-120	1	A:6-120
2	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	DCTD_RHIME	145-374	1	A:145-145

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	DCTD_RHIME	6-120	2	A:6-120
2	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	DCTD_RHIME	145-374	2	A:145-145

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	DCTD_RHIME	6-120	4	A:6-120
2	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	DCTD_RHIME	145-374	4	A:145-145

Exons (0, 0)

Sequences/Alignments

Asymmetric 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

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Chain A from PDB  Type:PROTEIN  Length:146
 aligned with DCTD_RHIME | P13632 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
           DCTD_RHIME     2 SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGLPLIG 147
               SCOP domains d1l5za_ A: Transcriptional regulatory protein DctD, receiver domain                                                                                SCOP domains
               CATH domains 1l5zA00 A:2-147  [code=3.40.50.2300, no name defined]                                                                                              CATH domains
               Pfam domains -----Response_reg-1l5zA01 A:7-117                                                                                   ------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhh.......eeeee......hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RESPONSE_REGULATORY  PDB: A:6-120 UniProt: 6-120                                                                   ------------------------SIG PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5z A   2 SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRSLRRAAEAASEGLKLAA 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Legend:		→ Mismatch	(orange background)
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	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)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (DCTD_RHIME | P13632)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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: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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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.
cellular component
	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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