3LA7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NTCA IN APO-FORM

Authors :   M. X. Zhao, Y. L. Jiang, Y. X. He, Y. F. Chen, Y. B. Teng, C. C. Zhang, Y. X. Ch C. Z. Zhou

Date :   06 Jan 10 (Deposition) - 01 Sep 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Nitrogen Regulator, Activator, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. X. Zhao, Y. L. Jiang, Y. X. He, Y. F. Chen, Y. B. Teng, Y. X. Chen, C. C. Zhang, C. Z. Zhou
Structural Basis For The Allosteric Control Of The Global Transcription Factor Ntca By The Nitrogen Starvation Signal 2-Oxoglutarate.
Proc. Natl. Acad. Sci. Usa V. 107 12487 2010
PubMed-ID: 20616047 | Reference-DOI: 10.1073/PNAS.1001556107

Molecule 1 - GLOBAL NITROGEN REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ALR4392, BIFA, NTCA
	Organism Scientific	:	ANABAENA
	Organism Taxid	:	103690
	Strain	:	PCC 7120
	Synonym	:	DNA-BINDING PROTEIN VF1, NITROGEN-RESPONSIVE REGULATORY PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:8 , PRO A:23 , VAL A:44 , ASN A:72 , LEU A:101 , LEU A:121 , MET A:122 , ARG A:124 , GLY A:125	BINDING SITE FOR RESIDUE BOG A 224

(no "SS Bond" information available for 3LA7)

(no "Cis Peptide Bond" information available for 3LA7)

(no "SAP(SNP)/Variant" information available for 3LA7)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	NTCA_NOSS1	28-129	2	A:28-129 B:28-129
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	NTCA_NOSS1	143-216	2	A:143-214 B:143-216
3	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	NTCA_NOSS1	174-197	2	A:174-197 B:174-197

(no "Exon" information available for 3LA7)

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:209
 aligned with NTCA_NOSS1 | P0A4U6 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:209
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
           NTCA_NOSS1     6 DKALANVFRQMATGAFPPVVETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHK 214
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh......eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh.......eeeee...eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheee....eee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: A:28-129 UniProt: 28-129                                                         -------------HTH_CRP_2  PDB: A:143-214 UniProt: 143-216                               PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:174-19----------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la7 A   6 DKALANVFRQMATGAFPPVVETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHK 214
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with NTCA_NOSS1 | P0A4U6 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:211
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215 
           NTCA_NOSS1     6 DKALANVFRQMATGAFPPVVETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPV 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------cNMP_binding-3la7B03 B:25-117                                                                -----------------------------HTH_Crp_2-3la7B01 B:147-216                                            Pfam domains (1)
           Pfam domains (2) -------------------cNMP_binding-3la7B04 B:25-117                                                                -----------------------------HTH_Crp_2-3la7B02 B:147-216                                            Pfam domains (2)
         Sec.struct. author hhhhhhhhhh.------.eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh.......eeeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheee....eee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: B:28-129 UniProt: 28-129                                                         -------------HTH_CRP_2  PDB: B:143-216 UniProt: 143-216                                 PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:174-19------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la7 B   6 DKALANVFRQM------PVVETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPV 216
                                    15|      |25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215 
                                     16     23

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 3LA7)

(no "CATH Domain" information available for 3LA7)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_Crp_2 (9)

Nostoc sp. (strain PCC 7120 / UTEX 2576) (3)

1a	HTH_Crp_2-3la7B01	B:147-216
1b	HTH_Crp_2-3la7B02	B:147-216

Clan: no clan defined [family: cNMP_binding] (41)

Family: cNMP_binding (41)

Nostoc sp. (strain PCC 7120 / UTEX 2576) (3)

2a	cNMP_binding-3la7B03	B:25-117
2b	cNMP_binding-3la7B04	B:25-117

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NTCA_NOSS1 | P0A4U6)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
biological process
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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
		BOG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3la7)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3la7
		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
	NTCA_NOSS1 \| P0A4U6
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NTCA_NOSS1 \| P0A4U6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NTCA_NOSS1 \| P0A4U6	:	3la2 3la3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File