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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF NTCA WITH ITS TRANSCRIPTIONAL CO-ACTIVATOR PIPX

Authors :   J. L. Llacer, M. A. Castells, V. Rubio

Date :   11 Jul 10 (Deposition) - 18 Aug 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Transcription, Nitrogen Assimilation, Crp/Fnr Superfamily, 2-Oxoglutarate, Global Nitrogen Controller (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Llacer, J. Espinosa, M. A. Castells, A. Contreras, K. Forchhammer, V. Rubio
Structural Basis For The Regulation Of Ntca- Dependent Transcription By Proteins Pipx And Pii.
Proc. Natl. Acad. Sci. Usa V. 107 15397 2010
PubMed-ID: 20716687 | Reference-DOI: 10.1073/PNAS.1007015107

Molecule 1 - GLOBAL NITROGEN REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942
	Synonym	:	NTCA

Molecule 2 - PIPX
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:53 , PHE A:74 , GLY A:75 , VAL A:76 , LEU A:77 , ARG A:87 , ARG A:128 , HOH A:2037 , ILE B:129 , GLU B:133	BINDING SITE FOR RESIDUE AKG A1223
2	AC2	SOFTWARE	ILE A:129 , LEU A:130 , GLU A:133 , LEU B:53 , PHE B:74 , GLY B:75 , VAL B:76 , LEU B:77 , ARG B:87 , ARG B:128 , HOH B:2034	BINDING SITE FOR RESIDUE AKG B1223

(no "SS Bond" information available for 2XKO)

Asymmetric/Biological Unit

No.	Residues
1	Arg C:45	-	Gly C:46
2	Gly D:22	-	Asp D:23
3	Arg D:45	-	Gly D:46

(no "SAP(SNP)/Variant" information available for 2XKO)

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_SYNE7	22-128	2	A:22-128 B:22-128
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	NTCA_SYNE7	142-215	2	A:142-215 B:142-215
3	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	NTCA_SYNE7	173-196	2	A:173-196 B:173-196

(no "Exon" information available for 2XKO)

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:212
 aligned with NTCA_SYNE7 | P29283 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:212
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
           NTCA_SYNE7    11 MFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......eeeee..eeeee.......eeeeeee.eeeeeeee...eeeeeeee....ee..hhhhhh.......eeee...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------CNMP_BINDING_3  PDB: A:22-128 UniProt: 22-128                                                              -------------HTH_CRP_2  PDB: A:142-215 UniProt: 142-215                                ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:173-19-------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xko A  11 MFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NTCA_SYNE7 | P29283 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:212
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
           NTCA_SYNE7    11 MFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------cNMP_binding-2xkoB03 B:24-116                                                                -----------------------------HTH_Crp_2-2xkoB01 B:146-220                                                -- Pfam domains (1)
           Pfam domains (2) -------------cNMP_binding-2xkoB04 B:24-116                                                                -----------------------------HTH_Crp_2-2xkoB02 B:146-220                                                -- Pfam domains (2)
         Sec.struct. author hhhhhh......eeeee..eeeee.......eeeeeee.eeeeeeee...eeeeeeee....ee..hhhhhh.......eeee...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------CNMP_BINDING_3  PDB: B:22-128 UniProt: 22-128                                                              -------------HTH_CRP_2  PDB: B:142-215 UniProt: 142-215                                ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:173-19-------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xko B  11 MFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with Q7X386_SYNE7 | Q7X386 from UniProtKB/TrEMBL  Length:89

    Alignment length:86
                                    13        23        33        43        53        63        73        83      
         Q7X386_SYNE7     4 ENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeeeee.-.eeeeee.....eeeeee......eeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2xko C   4 ENYLNHPTFGLLYQICSFG-SKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
                                    13        |-|       33        43        53        63        73        83      
                                             22 |                                                                 
                                               24

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with Q7X386_SYNE7 | Q7X386 from UniProtKB/TrEMBL  Length:89

    Alignment length:86
                                    13        23        33        43        53        63        73        83      
         Q7X386_SYNE7     4 ENYLNHPTFGLLYQICSFGDSKELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF3539-2xkoD01 D:4- 89                                                                Pfam domains (1)
           Pfam domains (2) DUF3539-2xkoD02 D:4- 89                                                                Pfam domains (2)
         Sec.struct. author .eeeee...eeeeeeeee..-eeeeee.....eeeeee......eeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2xko D   4 ENYLNHPTFGLLYQICSFGD-KELFATLYAQRLFFLVAFDARGTRFEPIGRNEARMLVDNRLRQLRRDASLQEYNQLQQVFKQTFL  89
                                    13        23 |      33        43        53        63        73        83      
                                              23 |                                                                
                                                25

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 2XKO)

(no "CATH Domain" information available for 2XKO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NTCA_SYNE7 | P29283)

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.

Chain C,D (Q7X386_SYNE7 | Q7X386)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg C:45 - Gly C:46	[ RasMol ]
		Arg D:45 - Gly D:46	[ RasMol ]
		Gly D:22 - Asp D:23	[ RasMol ]

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	2xko
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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	NTCA_SYNE7 \| P29283
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		Protein-protein Interaction	:	DIP
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	Q7X386_SYNE7 \| Q7X386
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	NTCA_SYNE7 \| P29283
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	Q7X386_SYNE7 \| Q7X386
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NTCA_SYNE7 \| P29283	:	2xgx 2xhk 2xkp
UniProtKB/TrEMBL
	Q7X386_SYNE7 \| Q7X386	:	2xg8

2xg8	STRUCTURAL BASIS OF GENE REGULATION BY PROTEIN PII: THE CRYSTAL COMPLEX OF PII AND PIPX FROM SYNECHOCOCCUS ELONGATUS PCC 7942
2xgx	CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR NTCA FROM SYNECHOCOCCUS ELONGATUS (MERCURY DERIVATIVE)
2xhk	CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR NTCA FROM SYNECHOCOCCUS ELONGATUS BOUND TO 2- OXOGLUTARATE
2xkp	NTCA FROM SYNECHOCOCCUS ELONGATUS: ACTIVE AND INACTIVE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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 (3, 6)

Gene Ontology (5, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File