1L5Y - JenaLib

Title :   CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND 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 :   2.10

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

Keywords :   Beryllofluoride Bound Two Component Receiver Domain, 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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 21)

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:12 , ASP A:55 , ARG A:57 , BEF A:660 , HOH A:709 , HOH A:710	BINDING SITE FOR RESIDUE MG A 701
02	AC2	SOFTWARE	ASP B:212 , ASP B:255 , ARG B:257 , BEF B:661 , HOH B:743 , HOH B:744	BINDING SITE FOR RESIDUE MG B 702
03	AC3	SOFTWARE	LYS A:69 , ARG B:214 , ARG B:217 , ALA B:235 , HOH B:746 , HOH B:747 , HOH B:770	BINDING SITE FOR RESIDUE SO4 B 703
04	AC4	SOFTWARE	ARG A:133 , BF2 A:662 , ALA B:265 , LYS B:269	BINDING SITE FOR RESIDUE SO4 B 704
05	AC5	SOFTWARE	SER A:36 , THR A:38 , PRO A:59 , GLY A:60 , HOH A:739 , HOH A:744 , HOH A:817 , LYS B:218 , GLN B:221 , GOL B:674 , HOH B:730	BINDING SITE FOR RESIDUE SO4 A 706
06	AC6	SOFTWARE	ASP A:13 , HIS A:85 , HOH A:709 , HOH A:710 , HOH A:720 , HOH A:806 , HIS B:351 , HIS B:352	BINDING SITE FOR RESIDUE SO4 A 707
07	AC7	SOFTWARE	ASP A:55 , ILE A:56 , ARG A:57 , THR A:83 , GLY A:84 , HIS A:85 , LYS A:105 , MG A:701 , HOH A:709	BINDING SITE FOR RESIDUE BEF A 660
08	AC8	SOFTWARE	ASP B:255 , ILE B:256 , ARG B:257 , THR B:283 , GLY B:284 , HIS B:285 , LYS B:305 , MG B:702 , HOH B:743	BINDING SITE FOR RESIDUE BEF B 661
09	AC9	SOFTWARE	GLU A:141 , ALA B:265 , ARG B:268 , LYS B:269 , SO4 B:704	BINDING SITE FOR RESIDUE BF2 A 662
10	BC1	SOFTWARE	LYS A:121 , ARG A:124	BINDING SITE FOR RESIDUE BF2 A 663
11	BC2	SOFTWARE	ILE A:95 , GLN A:96	BINDING SITE FOR RESIDUE BF2 A 664
12	BC3	SOFTWARE	ILE A:103 , ALA A:104 , ARG A:111 , HOH A:754 , HOH A:784 , PRO B:289	BINDING SITE FOR RESIDUE BF2 A 665
13	BC4	SOFTWARE	LEU A:73 , LYS B:321	BINDING SITE FOR RESIDUE BF2 B 666
14	BC5	SOFTWARE	TYR A:100 , LYS A:122	BINDING SITE FOR RESIDUE BF2 A 667
15	BC6	SOFTWARE	BF2 A:671 , ASP B:287 , ILE B:288	BINDING SITE FOR RESIDUE BF2 B 668
16	BC7	SOFTWARE	SER A:6 , THR A:30 , SER A:32	BINDING SITE FOR RESIDUE BF2 A 669
17	BC8	SOFTWARE	ARG A:133 , ALA A:139 , SER A:140 , HOH A:781	BINDING SITE FOR RESIDUE BF2 A 670
18	BC9	SOFTWARE	ASP A:87 , ILE A:88 , BF2 B:668	BINDING SITE FOR RESIDUE BF2 A 671
19	CC1	SOFTWARE	ALA A:108 , ALA A:109 , GLU B:337 , SER B:340 , HOH B:777	BINDING SITE FOR RESIDUE BEF B 672
20	CC2	SOFTWARE	ASP A:12 , ARG A:14 , ARG A:17 , ALA A:35 , HOH A:730	BINDING SITE FOR RESIDUE BF4 A 673
21	CC3	SOFTWARE	THR A:38 , GLU A:39 , SO4 A:706 , HOH A:744 , LYS B:218 , ASN B:329 , ARG B:333	BINDING SITE FOR RESIDUE GOL B 674

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:143
 aligned with DCTD_RHIME | P13632 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144   
           DCTD_RHIME     5 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGLPLIG 147
               SCOP domains d1l5ya_ A: Transcriptional regulatory protein DctD, receiver domain                                                                             SCOP domains
               CATH domains 1l5yA00 A:5-147  [code=3.40.50.2300, no name defined]                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhh.......eeeee......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: A:6-120 UniProt: 6-120                                                                   ------------------------SIG PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5y A   5 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRSLRRAAEAASEGLKLAA 147
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with DCTD_RHIME | P13632 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:161
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 
           DCTD_RHIME     3 AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGLPLIGQTPVMERLRQTLKHIA 163
               SCOP domains d1l5yb_ B: Transcriptional regulatory protein DctD, receiver domain                                                                                               SCOP domains
               CATH domains 1l5yB00 B:203-353  [code=3.40.50.2300, no name defined]                                                                                                           CATH domains
           Pfam domains (1) ----Response_reg-1l5yB01 B:207-317                                                                                 ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Response_reg-1l5yB02 B:207-317                                                                                 ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeeee......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RESPONSE_REGULATORY  PDB: B:206-320 UniProt: 6-120                                                                 ------------------------SIGMA54_INTERACT_4  PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l5y B 203 AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRSLRRAAEAASEGL----------KLAAALEHHH 353
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342|        - |     352 
                                                                                                                                                                      343        344

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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, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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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