1K6X - JenaLib

Title :   CRYSTAL STRUCTURE OF NMRA, A NEGATIVE TRANSCRIPTIONAL REGULATOR IN COMPLEX WITH NAD AT 1.5 A RESOLUTION (TRIGONAL FORM)

Authors :   D. K. Stammers, J. Ren, K. Leslie, C. E. Nichols, H. K. Lamb, S. Cocklin, A A. R. Hawkins

Date :   17 Oct 01 (Deposition) - 20 Feb 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

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

Reference :   D. K. Stammers, J. Ren, K. Leslie, C. E. Nichols, H. K. Lamb, S. Cocklin, A. Dodds, A. R. Hawkins
The Structure Of The Negative Transcriptional Regulator Nmr Reveals A Structural Superfamily Which Includes The Short-Chain Dehydrogenase/Reductases.
Embo J. V. 20 6619 2002
PubMed-ID: 11726498 | Reference-DOI: 10.1093/EMBOJ/20.23.6619
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:6 , HIS A:30 , ASN A:253 , HOH A:690	BINDING SITE FOR RESIDUE CL A 360
2	AC2	SOFTWARE	GLN A:48 , ILE A:50 , VAL A:53 , HOH A:521 , HOH A:731 , HOH A:1095	BINDING SITE FOR RESIDUE CL A 361
3	AC3	SOFTWARE	ARG A:139 , LEU A:141 , LEU A:143 , ASN A:346 , HOH A:953 , HOH A:959 , HOH A:1044	BINDING SITE FOR RESIDUE CL A 362
4	AC4	SOFTWARE	GLN A:106 , PRO A:208 , VAL A:252 , ASN A:253 , HOH A:410	BINDING SITE FOR RESIDUE CL A 363
5	AC5	SOFTWARE	ASN A:12 , THR A:14 , VAL A:36 , HIS A:37	BINDING SITE FOR RESIDUE CL A 401
6	AC6	SOFTWARE	SER A:38 , LYS A:40 , HOH A:511 , HOH A:563 , HOH A:778	BINDING SITE FOR RESIDUE CL A 402
7	AC7	SOFTWARE	ASN A:12 , THR A:14 , GLY A:15 , ARG A:16 , GLN A:17 , HIS A:37 , ASN A:80 , THR A:81 , THR A:82 , GLN A:84 , ALA A:85 , MET A:113 , LYS A:131 , ALA A:150 , GLY A:151 , ILE A:152 , TYR A:153 , ASN A:156 , TYR A:276 , HOH A:422 , HOH A:520 , HOH A:537 , HOH A:584 , HOH A:591 , HOH A:603 , HOH A:699 , HOH A:702 , HOH A:750 , HOH A:777 , HOH A:802	BINDING SITE FOR RESIDUE NAD A 400

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:324
 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 d1k6xa_ A: Negative transcriptional regulator NmrA                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1k6xA01 A:3-151,A:191-219,A:275-328 NAD(P)-binding Rossmann-like Domain                                                                              1k6xA02 A:152-190,A:220-274,A:329-351  1k6xA01                      1k6xA02 A:152-190,A:220-274,A:329-351                  1k6xA01                                               1k6xA02                - CATH domains
               Pfam domains -----NmrA-1k6xA01 A:8-244                                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee....hhhhhhhhhhhhhh...eeeee....hhhhhhhhh...eeeee........hh.hhhh...eeee.......hhhhhhhhhhhhhhhhh...eeeeee..hhhhh........hhhhhhhhhhhhh....eeeeee.ee.hhh.........eee.....eeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh.........hhhhh--------------------------........hhhhhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k6x A   3 QQKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFS--------------------------GGVISQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 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                        310

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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k6x)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1k6x
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NMRA_EMENI \| Q5AU62
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description