1OMI - JenaLib

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Title :   CRYSTAL STRUCTURE OF PRFA,THE TRANSCRIPTIONAL REGULATOR IN LISTERIA MONOCYTOGENES

Authors :   R. Thirumuruhan, K. Rajashankar, A. A. Fedorov, T. Dodatko, M. R. Chanc P. Cossart, S. C. Almo, S. K. Burley, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   25 Feb 03 (Deposition) - 11 Mar 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Transcriptional Regulator Prfa, Cap Fold, Listeria Monocytogenes, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Thirumuruhan, K. Rajashankar, A. A. Fedorov, T. Dodatko, M. R. Chance, P. Cossart, S. C. Almo
Crystal Structure Of Prfa, The Transcriptional Regulator In Listeria Monocytogenes
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - LISTERIOLYSIN REGULATORY PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PRFA OR LMO0200
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	1639

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:1029 , ASN A:1030 , ASP A:1033 , GLN A:1035 , GLU A:1036 , SER A:1071 , SER A:1079 , GLY A:1081 , TYR A:1082 , TYR A:1083	BINDING SITE FOR RESIDUE GOL A 3001
2	AC2	SOFTWARE	ASN B:2030 , ASP B:2033 , GLN B:2035 , GLU B:2036 , SER B:2071 , SER B:2079 , GLY B:2081 , TYR B:2082 , TYR B:2083 , ARG B:2188	BINDING SITE FOR RESIDUE GOL B 3002

(no "SS Bond" information available for 1OMI)

(no "Cis Peptide Bond" information available for 1OMI)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRFA_LISMO_001 *	G	145	S	PRFA_LISMO	---	---	A B	G	1145 2145	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRFA_LISMO_001 *	G	145	S	PRFA_LISMO	---	---	A A	G	1145 2145	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRFA_LISMO_001 *	G	145	S	PRFA_LISMO	---	---	A B	G	1145 2145	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PRFA_LISMO_001 *	G	145	S	PRFA_LISMO	---	---	A A/B	G	1145 2145	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	PRFA_LISMO	137-212	2	A:1137-1212 B:2137-2212
2	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	PRFA_LISMO	169-193	2	A:1169-1193 B:2169-2193

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	PRFA_LISMO	137-212	1	A:1137-1212 -
2	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	PRFA_LISMO	169-193	1	A:1169-1193 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	PRFA_LISMO	137-212	1	- B:2137-2212
2	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	PRFA_LISMO	169-193	1	- B:2169-2193

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	PRFA_LISMO	137-212	2	A:1137-1212 B:2137-2212
2	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	PRFA_LISMO	169-193	2	A:1169-1193 B:2169-2193

(no "Exon" information available for 1OMI)

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:224
 aligned with PRFA_LISMO | P22262 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:233
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   
          PRFA_LISMO      5 AEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN  237
               SCOP domains d1omia1 A:1005-1137 Listeriolysin regulatory protein PrfA, N-terminal domain                                                         d1omia2 A:1138-1237 Listeriolysin reg         ulatory protein PrfA, C-terminal domain                SCOP domains
               CATH domains 1omiA01 A:1005-1109 Jelly Rolls                                                                          1omiA02 A:1110-1136        1omiA03 A:1137-1237 'winged helix' rep         ressor DNA binding domain                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....ee.....eee.......eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee.....hhhhh---------hhhhhhhhhhhhh..eee....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: A:1137-1212 UniProt: 137-212                                ------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1                -------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1omi A 1005 GSEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQEL---------SAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 1237
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234   
                                                                                                                                                                                                  1174      1184

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with PRFA_LISMO | P22262 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:233
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   
          PRFA_LISMO      5 AEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN  237
               SCOP domains d1omib1 B:2005-2137 Listeriolysin regulatory protein PrfA, N-terminal domain                                                         d1omib2 B:2138-2237 Listeriolysin regul      atory protein PrfA, C-terminal domain                   SCOP domains
               CATH domains 1omiB01 B:2005-2109 Jelly Rolls                                                                          ---------------------------1omiB02 B:2137-2237 'winged helix' repre      ssor DNA binding domain                                 CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------HTH_Crp_2-1omiB01 B:2141-2217                                                -------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------HTH_Crp_2-1omiB02 B:2141-2217                                                -------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh....eeee...eee.......eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee...eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.....eee..hhhhhhh...------.hhhhhhhhhhhhh..eee....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: B:2137-2212 UniProt: 137-212                                ------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1                -------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1omi B 2005 GSEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGY------SSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 2237
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174 |    2184      2194      2204      2214      2224      2234   
                                                                                                                                                                                                    2176   2183

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_Crp_2 (9)

Listeria monocytogenes (1)

1a	HTH_Crp_2-1omiB01	B:2141-2217
1b	HTH_Crp_2-1omiB02	B:2141-2217

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRFA_LISMO | P22262)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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.

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	PRFA_LISMO \| P22262	:	2beo 2bgc 5f1r 5lej 5lek 5lrr 5lrs

(no "Related Entries Specified in the PDB File" available for 1OMI)

Description

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