2NZV - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURAL MECHANISM FOR THE FINE-TUNING OF CCPA FUNCTION BY THE SMALL MOLECULE EFFECTORS G6P AND FBP

Authors :   M. A. Schumacher, W. Hillen, R. G. Brennan

Date :   25 Nov 06 (Deposition) - 01 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : G,L
Biol. Unit 1: G,L  (2x)

Keywords :   Ccpa, Hprser46-P, Ccr, Fructose-Bis-Phosphate, Adjunct Corepressor, Laci-Galr, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, G. Seidel, W. Hillen, R. G. Brennan
Structural Mechanism For The Fine-Tuning Of Ccpa Function By The Small Molecule Effectors Glucose 6-Phosphate And Fructose 1, 6-Bisphosphate.
J. Mol. Biol. V. 368 1042 2007
PubMed-ID: 17376479 | Reference-DOI: 10.1016/J.JMB.2007.02.054
(for further references see the PDB file header)

Molecule 1 - CATABOLITE CONTROL PROTEIN
	Chains	:	G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 53-332
	Gene	:	CCPA
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404

Molecule 2 - PHOSPHOCARRIER PROTEIN HPR
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PTSH
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Synonym	:	HISTIDINE-CONTAINING PROTEIN

		1	2
Asymmetric Unit	:	G	L
Biological Unit 1 (2x)	:	G	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	FBP	1	Ligand/Ion	BETA-FRUCTOSE-1,6-DIPHOSPHATE
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	FBP	2	Ligand/Ion	BETA-FRUCTOSE-1,6-DIPHOSPHATE
2	SEP	2	Mod. Amino Acid	PHOSPHOSERINE
3	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE G:73 , PHE G:74 , TYR G:75 , GLN G:100 , TYR G:221 , THR G:247 , GLU G:249 , ASP G:275	BINDING SITE FOR RESIDUE FBP G 2128
2	AC2	SOFTWARE	THR G:313	BINDING SITE FOR RESIDUE SO4 G 745
3	AC3	SOFTWARE	LYS G:195	BINDING SITE FOR RESIDUE SO4 G 945
4	AC4	SOFTWARE	ASN G:152 , ARG G:212 , ASP G:213 , SER G:214 , ILE G:318	BINDING SITE FOR RESIDUE SO4 G 946
5	AC5	SOFTWARE	HIS G:193 , LYS G:198	BINDING SITE FOR RESIDUE SO4 G 966
6	AC6	SOFTWARE	ASP L:11 , SER L:12	BINDING SITE FOR RESIDUE SO4 L 975
7	AC7	SOFTWARE	GLN L:3 , LYS L:4 , THR L:5	BINDING SITE FOR RESIDUE SO4 L 978
8	AC8	SOFTWARE	ARG G:328 , ASP L:11	BINDING SITE FOR RESIDUE SO4 G 995

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

Asymmetric Unit

No.	Residues
1	Val G:265	-	Pro G:266
2	Arg G:284	-	Pro G:285

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTS_HPR_HIS	PS00369	PTS HPR domain histidine phosphorylation site signature.	PTHP_BACME	13-20	1	L:13-20
2	PTS_HPR_SER	PS00589	PTS HPR domain serine phosphorylation site signature.	PTHP_BACME	39-54	1	L:39-54

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTS_HPR_HIS	PS00369	PTS HPR domain histidine phosphorylation site signature.	PTHP_BACME	13-20	2	L:13-20
2	PTS_HPR_SER	PS00589	PTS HPR domain serine phosphorylation site signature.	PTHP_BACME	39-54	2	L:39-54

(no "Exon" information available for 2NZV)

Asymmetric 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
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Chain G from PDB  Type:PROTEIN  Length:275
 aligned with CCPA_BACME | P46828 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:275
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
           CCPA_BACME    58 KKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK 332
               SCOP domains d2nzvg_ G: Glucose-resistance amylase regulator CcpA, C-terminal domain                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------Peripla_BP_3-2nzvG01 G:169-331                                                                                                                                     - Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh....eee.....hhhhhhhh......eeee..........eeeehhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.........ee....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhh.......eee.hhhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nzv G  58 KKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK 332
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327

Chain L from PDB  Type:PROTEIN  Length:87
 aligned with PTHP_BACME | O69250 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           PTHP_BACME     2 AQKTFTVTADSGIHARPATTLVQAASKFDSDINLEFNGKTVNLKSIMGVMSLGIQKGATITISAEGSDEADALAALEDTMSKEGLGE  88
               SCOP domains d2nzvl_ L: Histidine-containing phosphocarrier protein (HPr)                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains PTS-HPr-2nzvL01 L:2-84                                                             ---- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhh.......eeeee..eee...hhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PTS_HPR_------------------PTS_HPR_SER     ---------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2nzv L   2 AQKTFTVTADSGIHARPATTLVQAASKFDSDINLEFNGKTVNLKsIMGVMSLGIQKGATITISAEGSDEADALAALEDTMSKEGLGE  88
                                    11        21        31        41    |   51        61        71        81       
                                                                       46-SEP

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 "CATH Domain" information available for 2NZV)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Bacillus megaterium (7)

Peripla_BP_3-2nzvG01

G:169-331

Clan: no clan defined [family: PTS-HPr] (26)

Family: PTS-HPr (26)

Bacillus megaterium (3)

PTS-HPr-2nzvL01

L:2-84

Asymmetric Unit(hide GO term definitions)

Chain G (CCPA_BACME | P46828)

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.

Chain L (PTHP_BACME | O69250)

molecular function
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0008643	carbohydrate transport	The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
	GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	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.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Arg G:284 - Pro G:285	[ RasMol ]
		Val G:265 - Pro G:266	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2nzv
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	PTHP_BACME \| O69250
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UniProtKB/Swiss-Prot
	CCPA_BACME \| P46828	:	1rzr 1sxg 1sxh 1sxi 1zvv 2hsg 2jcg 2nzu 2oen
	PTHP_BACME \| O69250	:	1rzr 2nzu 2oen

1rzr	CCPA-HPRSER46P-CRE COMPLEX
1sxg	APO CCPA CORE
1sxh	APO CCPA CORE
1sxi	APO CCPA CORE
1zvv	CCPA-CRHSER46P-CRE COMPLEX
2nzu

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (13, 15)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File