1XGK - JenaLib

Title :   CRYSTAL STRUCTURE OF N12G AND A18G MUTANT NMRA

Authors :   H. K. Lamb, J. Ren, A. Park, C. Johnson, K. Leslie, S. Cocklin, P. Thompso A. Cooper, D. K. Stammers, A. R. Hawkins

Date :   17 Sep 04 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Rossmann Fold, Transcriptional Regulation, Short Chain Dehydrogenase, Reductase, Nadp Binding, Nmra, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. K. Lamb, J. Ren, A. Park, C. Johnson, K. Leslie, S. Cocklin, P. Thompson, C. Mee, A. Cooper, D. K. Stammers, A. R. Hawkins
Modulation Of The Ligand Binding Properties Of The Transcription Repressor Nmra By Gata-Containing Dna And Site-Directed Mutagenesis
Protein Sci. V. 13 3127 2004
PubMed-ID: 15537757 | Reference-DOI: 10.1110/PS.04958904
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:16 , TYR A:153 , HOH A:1222 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2043 , HOH A:2044	BINDING SITE FOR RESIDUE PO4 A 502
02	AC2	SOFTWARE	GLN A:48 , ILE A:50 , PRO A:51 , VAL A:53 , HOH A:1373 , HOH A:1396 , HOH A:2010	BINDING SITE FOR RESIDUE K A 503
03	AC3	SOFTWARE	ARG A:139 , LEU A:141 , ASN A:346 , HOH A:1006 , HOH A:1151 , HOH A:1262 , HOH A:1329	BINDING SITE FOR RESIDUE K A 504
04	AC4	SOFTWARE	GLN A:106 , PRO A:208 , VAL A:252 , ASN A:253 , HOH A:969	BINDING SITE FOR RESIDUE CL A 505
05	AC5	SOFTWARE	GLN A:166 , LYS A:251 , HOH A:1524	BINDING SITE FOR RESIDUE CL A 506
06	AC6	SOFTWARE	SER A:38 , LEU A:39 , GLN A:57 , GLN A:315	BINDING SITE FOR RESIDUE CL A 507
07	AC7	SOFTWARE	ARG A:33 , HOH A:973 , HOH A:1333 , HOH A:1486 , HOH A:1527	BINDING SITE FOR RESIDUE CL A 964
08	AC8	SOFTWARE	GLN A:140 , GLY A:347 , ASP A:349 , HOH A:1097 , HOH A:1136 , HOH A:1497	BINDING SITE FOR RESIDUE K A 965
09	AC9	SOFTWARE	SER A:111 , SER A:112 , VAL A:148 , TYR A:149 , ALA A:150 , HOH A:1064	BINDING SITE FOR RESIDUE K A 966
10	BC1	SOFTWARE	LYS A:6 , HIS A:30 , ASN A:253 , HOH A:1164 , HOH A:1427	BINDING SITE FOR RESIDUE CL A 2040
11	BC2	SOFTWARE	PRO A:198 , LEU A:201 , GLN A:202 , LYS A:205 , LEU A:324 , TRP A:325 , GLU A:344 , HOH A:993 , HOH A:1048 , HOH A:1171 , HOH A:1239	BINDING SITE FOR RESIDUE GOL A 501

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 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:325
 aligned with NMRA_EMENI | Q5AU62 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:350
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
           NMRA_EMENI     3 QQKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFSRPAAGSPKGLGPANGKGAGAGMMQGPGGVISQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
               SCOP domains d1xgka_ A: Negative transcriptional regulator NmrA                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xgkA01 A:3-151,A:191-219,A:275-328 NAD(P)-binding Rossmann-like Domain                                                                              1xgkA02 A:152-190,A:220-274,A:329-351  1xgkA01                      1xgkA02 A:152-190,A:220-274,A:329-351                  1xgkA01 A                         :3-151,A:191-219,A:21xgkA02                - CATH domains
               Pfam domains -----NmrA-1xgkA01 A:8-244                                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee...hhhhhhhhhhhhhh...eeeee....hhhhhhhhh...eeeee.....hhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh...eeeeee..hhhhh........hhhhhhhhhhhhh....eeeeee.ee.hhh.........eee.....eeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh........hhhhh-------------------------.........hhhhhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xgk A   3 QQKKTIAVVGATGRQGASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFS-------------------------PGGVISQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282|        -         -      |312       322       332       342       352
                                                                                                                                                                                                                                                                                                                  283                       309

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)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NMRA_EMENI | Q5AU62)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0070404	NADH binding	Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0070402	NADPH binding	Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0070405	ammonium ion binding	Interacting selectively and non-covalently with ammonium ions (NH4+).
	GO:0070406	glutamine binding	Interacting selectively and non-covalently with glutamine, 2,5-diamino-5-oxopentanoic acid.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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).
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0090295	nitrogen catabolite repression of transcription	A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
	GO:0001081	nitrogen catabolite repression of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006808	regulation of nitrogen utilization	Any process that modulates the frequency, rate or extent of nitrogen utilization.
	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.
	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.

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