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Title :   CRYSTAL STRUCTURE OF PROPIONATE CATABOLISM OPERON REGULATORY PROTEIN PRPR

Authors :   U. A. Ramagopal, R. Toro, M. Gilmore, B. Wu, J. Koss, C. Groshong, T. Gheyi, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   16 Apr 07 (Deposition) - 22 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Structural Genomics, Prpr, Transcriptional Regulation, Psi- 2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. A. Ramagopal, R. Toro, M. Gilmore, B. Wu, J. Koss, C. Groshong, T. Gheyi, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Propionate Catabolism Operon Regulatory Protein Prpr
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROPIONATE CATABOLISM OPERON REGULATORY PROTEIN
	Atcc	:	47076
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BC-PSSGX3(BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PRPR, B0330, JW0322
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	K12, MG1655

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2PJU)

(no "Site" information available for 2PJU)

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

(no "Cis Peptide Bond" information available for 2PJU)

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	PRPR_ECOLI	218-460	1	D:216-220

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	PRPR_ECOLI	218-460	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIGMA54_INTERACT_4	PS50045	Sigma-54 interaction domain profile.	PRPR_ECOLI	218-460	1	D:216-220

(no "Exon" information available for 2PJU)

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
	(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:186
 aligned with PRPR_ECOLI | P77743 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:186
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
           PRPR_ECOLI    11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMS 196
               SCOP domains d2pjua1 A:11-196 Propionate catabolism operon regulatory protein PrpR                                                                                                                      SCOP domains
               CATH domains 2pjuA01 A:11-88,A:177-196  [code=3.40.50.2300, no name defined]               2pjuA02 A:89-176 PrpR receptor domain-like                                              2pjuA01              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhh......eeeeehhhhhhhhh.....eeee..hhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pju A  11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQFLAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMS 196
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with PRPR_ECOLI | P77743 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:187
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
           PRPR_ECOLI    11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSL 197
               SCOP domains d2pjub_ B: Propionate catabolism operon regulatory protein PrpR                                                                                                                             SCOP domains
               CATH domains 2pjuB01 B:11-88,B:177-197  [code=3.40.50.2300, no name defined]               2pjuB02 B:89-176 PrpR receptor domain   -like                                           2pjuB01               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh...eeee..hhhhhhhhhhhhh.....eeeeee.....hhhhhhhh---.eeeeee.hhhhhhhhhhhhhh....eeeehhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pju B  11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQFLAKAGKLTSSIGVVTYQETIPALVAFQKT---RLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSL 197
                                    20        30        40        50        60        70        80        90       100       110       120    |  130       140       150       160       170       180       190       
                                                                                                                                            125 129

Chain C from PDB  Type:PROTEIN  Length:188
 aligned with PRPR_ECOLI | P77743 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:188
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           PRPR_ECOLI    11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSLR 198
               SCOP domains d2pjuc_ C: Propionate catabolism operon regulatory protein PrpR                                                                                                                              SCOP domains
               CATH domains 2pjuC01 C:11-88,C:177-198  [code=3.40.50.2300, no name defined]               2pjuC02 C:89-176 PrpR receptor domain-like                                              2pjuC01                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeee..hhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pju C  11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQFLAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSLR 198
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:208
 aligned with PRPR_ECOLI | P77743 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:253
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
           PRPR_ECOLI    11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSLRHNTHDATRNALRTRYVLGDMLGQSPQMEQVRQTILLYARSSAAVLIEGETGTGKELAAQAIHREY 263
               SCOP domains d2pjud1 D:11-196 Propionate catabolism operon regulatory protein PrpR                                                                                                                     ------------------------------------------------------------------- SCOP domains
               CATH domains 2pjuD01 D:11-88  [code=3.40.50.2300, no name defined]                         2pjuD02 D:89-177 PrpR receptor domain-like                                               2pjuD03 D:178-223                                                                      CATH domains
           Pfam domains (1) -----------------PrpR_N-2pjuD01 D:28-202                                                                                                                                                        ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------PrpR_N-2pjuD02 D:28-202                                                                                                                                                        ------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------PrpR_N-2pjuD03 D:28-202                                                                                                                                                        ------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------PrpR_N-2pjuD04 D:28-202                                                                                                                                                        ------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee...hhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh.....eeeeehhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh-----hhhhh-----------------------------hhhh-----------hhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SIGMA54_INTERACT_4  PDB: D:216-220             PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pju D  11 KPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANERCDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQFLAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAATVRQAFSDALDMTRMSLRHNTHDAT-----TRYVL-----------------------------EGHH-----------HHHH 223
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    |    -|   |    -         -         -    |  | -       220   
                                                                                                                                                                                                                            205   211 215                           216  |         220   
                                                                                                                                                                                                                                                                       219

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Chelatase-like (149)

Superfamily: PrpR receptor domain-like (1)

Family: PrpR receptor domain-like (1)

Protein domain: Propionate catabolism operon regulatory protein PrpR (1)

Escherichia coli [TaxId: 562] (1)

1a	d2pjua1	A:11-196
1b	d2pjub_	B:
1c	d2pjuc_	C:
1d	d2pjud1	D:11-196

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PrpR_N] (2)

Family: PrpR_N (2)

Escherichia coli (strain K12) (1)

1a	PrpR_N-2pjuD01	D:28-202
1b	PrpR_N-2pjuD02	D:28-202
1c	PrpR_N-2pjuD03	D:28-202
1d	PrpR_N-2pjuD04	D:28-202

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PRPR_ECOLI | P77743)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000156	phosphorelay response regulator activity	Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0019629	propionate catabolic process, 2-methylcitrate cycle	The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
	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.

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