2FXA - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE PROTEASE PRODUCTION REGULATORY PROTEIN HPR FROM BACILLUS SUBTILIS.

Authors :   M. E. Cuff, T. Skarina, A. Edwards, A. Savchenko, A. Joachimiak, Midwes For Structural Genomics (Mcsg)

Date :   03 Feb 06 (Deposition) - 14 Mar 06 (Release) - 09 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Bacillus Subtilis, Hpr, Protease Porduction, Regulation, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, T. Skarina, A. Edwards, A. Savchenko, A. Joachimiak
Structure Of The Protease Production Regulatory Protein Hpr From Bacillus Subtilis.
To Be Published
PubMed: search

Molecule 1 - PROTEASE PRODUCTION REGULATORY PROTEIN HPR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	P11
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HPR, CATA, SCOC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 42)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (4, 18)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (5, 42)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:164 , SER A:167 , VAL B:15 , GLN B:18 , LYS B:19 , HOH B:347	BINDING SITE FOR RESIDUE EDO B 206
02	AC2	SOFTWARE	GLU A:147 , PHE B:139 , GLU C:147 , PHE D:139	BINDING SITE FOR RESIDUE EDO A 206
03	AC3	SOFTWARE	VAL C:145 , GLU C:147 , MSE C:148 , VAL D:145 , GLU D:147 , MSE D:148 , HOH D:324	BINDING SITE FOR RESIDUE EDO D 206
04	AC4	SOFTWARE	VAL A:145 , ALA A:146 , GLU A:147 , MSE A:148 , VAL B:145 , GLU B:147 , MSE B:148	BINDING SITE FOR RESIDUE EDO A 207
05	AC5	SOFTWARE	VAL B:74 , SER B:75 , PHE B:78	BINDING SITE FOR RESIDUE EDO B 207
06	AC6	SOFTWARE	GLU A:144 , GLU C:147 , LYS D:141 , GLU D:144	BINDING SITE FOR RESIDUE EDO A 208
07	AC7	SOFTWARE	PHE A:139 , GLU B:147 , GLU D:147	BINDING SITE FOR RESIDUE EDO B 208
08	AC8	SOFTWARE	PHE C:121 , ASP C:122 , ARG C:125 , PGE C:301	BINDING SITE FOR RESIDUE EDO C 208
09	AC9	SOFTWARE	GLU C:144 , LYS D:19	BINDING SITE FOR RESIDUE EDO C 209
10	BC1	SOFTWARE	PHE C:129 , GLN C:133 , TYR C:136 , PHE C:142 , TYR D:8 , ASP D:9 , GLU D:12	BINDING SITE FOR RESIDUE EDO D 210
11	BC2	SOFTWARE	GLU A:32 , EDO A:212 , LYS B:29	BINDING SITE FOR RESIDUE EDO B 211
12	BC3	SOFTWARE	ASN A:47 , HOH A:313 , EDO B:211	BINDING SITE FOR RESIDUE EDO A 212
13	BC4	SOFTWARE	GLU A:147 , HOH A:305 , PRO B:143 , GLU B:144 , GLU C:144 , ALA C:146	BINDING SITE FOR RESIDUE EDO A 213
14	BC5	SOFTWARE	PRO A:143 , GLU A:144 , GLU B:147 , GLU D:144 , ALA D:146	BINDING SITE FOR RESIDUE EDO A 214
15	BC6	SOFTWARE	TRP C:53 , ASN C:126 , EDO C:208 , GLN D:18 , ALA D:21 , GLN D:22	BINDING SITE FOR RESIDUE PGE C 301
16	BC7	SOFTWARE	THR A:17 , GLN A:18 , ALA A:21 , TRP B:35 , TRP B:38 , TRP B:53 , GLN B:57 , GLU B:120 , ASP B:122 , ASN B:126	BINDING SITE FOR RESIDUE P6G B 302
17	BC8	SOFTWARE	THR C:17 , GLN C:18 , ALA C:21 , GLN C:22 , TRP D:35 , TRP D:38 , TRP D:53 , PHE D:121 , ASP D:122 , ASN D:126	BINDING SITE FOR RESIDUE 1PE D 303
18	BC9	SOFTWARE	TRP A:35 , TRP A:38 , PHE A:121 , ASP A:122 , ASN A:126 , HOH A:325 , HOH A:349 , GLN B:18 , GLN B:22	BINDING SITE FOR RESIDUE 1PE A 304

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	HPR_BACSU	13-157	4	A:13-157 B:13-157 C:13-157 D:13-157
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	HPR_BACSU	76-110	4	A:76-110 B:76-110 C:76-110 D:76-110

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	HPR_BACSU	13-157	2	A:13-157 B:13-157 - -
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	HPR_BACSU	76-110	2	A:76-110 B:76-110 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	HPR_BACSU	13-157	2	- - C:13-157 D:13-157
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	HPR_BACSU	76-110	2	- - C:76-110 D:76-110

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MARR_2	PS50995	MarR-type HTH domain profile.	HPR_BACSU	13-157	4	A:13-157 B:13-157 C:13-157 D:13-157
2	HTH_MARR_1	PS01117	MarR-type HTH domain signature.	HPR_BACSU	76-110	4	A:76-110 B:76-110 C:76-110 D:76-110

(no "Exon" information available for 2FXA)

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:156
 aligned with HPR_BACSU | P11065 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:162
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165  
            HPR_BACSU     6 PPYDVKEALVFTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEMMCMIRHIYGDDFMEIFETS 167
               SCOP domains d2fxaa1 A:6-167 Protease production regulatory protein Hpr                                                                                                         SCOP domains
               CATH domains 2fxaA00 A:6-167 'winged helix' repressor DNA binding domain                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh..eeee..------.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------HTH_MARR_2  PDB: A:13-157 UniProt: 13-157                                                                                                        ---------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------HTH_MARR_1  PDB: A:76-110          --------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fxa A   6 PPYDVKEALVFTQKmAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVmHVSTAFNFSKKLEERGYLRFSKR------TYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEmmCmIRHIYGDDFmEIFETS 167
                                    15    |   25        35        45        55        65      | 75        85        95      |105       115       125       135       145  || | 155     | 165  
                                         20-MSE                                              72-MSE                 95    102                                           148-MSE      161-MSE  
                                                                                                                                                                         149-MSE              
                                                                                                                                                                           151-MSE

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with HPR_BACSU | P11065 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:180
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187
            HPR_BACSU     8 YDVKEALVFTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEMMCMIRHIYGDDFMEIFETSLTNIDNDFESVNGKLKKKAK 187
               SCOP domains d2fxab_ B: Protease production regulatory protein Hpr                                                                                                                                SCOP domains
               CATH domains 2fxaB00 B:8-187 'winged helix' repressor DNA binding domain                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----HTH_MARR_2  PDB: B:13-157 UniProt: 13-157                                                                                                        ------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------HTH_MARR_1  PDB: B:76-110          ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fxa B   8 YDVKEALVFTQKmAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVmHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEmmCmIRHIYGDDFmEIFETSLTNIDNDFESVNGKLKKKAK 187
                                    17  |     27        37        47        57        67    |   77        87        97       107       117       127       137       147|| |   157   |   167       177       187
                                       20-MSE                                              72-MSE                                                                     148-MSE      161-MSE                      
                                                                                                                                                                       149-MSE                                  
                                                                                                                                                                         151-MSE

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with HPR_BACSU | P11065 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:160
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167
            HPR_BACSU     8 YDVKEALVFTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEMMCMIRHIYGDDFMEIFETS 167
               SCOP domains d2fxac_ C: Protease production regulatory protein Hpr                                                                                                            SCOP domains
               CATH domains 2fxaC00 C:8-167 'winged helix' repressor DNA binding domain                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee....hhhh.eeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----HTH_MARR_2  PDB: C:13-157 UniProt: 13-157                                                                                                        ---------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------HTH_MARR_1  PDB: C:76-110          --------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fxa C   8 YDVKEALVFTQKmAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVmHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEmmCmIRHIYGDDFmEIFETS 167
                                    17  |     27        37        47        57        67    |   77        87        97       107       117       127       137       147|| |   157   |   167
                                       20-MSE                                              72-MSE                                                                     148-MSE      161-MSE  
                                                                                                                                                                       149-MSE              
                                                                                                                                                                         151-MSE

Chain D from PDB  Type:PROTEIN  Length:156
 aligned with HPR_BACSU | P11065 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166   
            HPR_BACSU     7 PYDVKEALVFTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEMMCMIRHIYGDDFMEIFETSLT 169
               SCOP domains d2fxad_ D: Protease production regulatory protein Hpr                                                                                                               SCOP domains
               CATH domains 2fxaD00 D:7-169 'winged helix' repressor DNA binding domain                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.-------.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------HTH_MARR_2  PDB: D:13-157 UniProt: 13-157                                                                                                        ------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------HTH_MARR_1  PDB: D:76-110          ----------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fxa D   7 PYDVKEALVFTQKmAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNGASISEIAKFGVmHVSTAFNFSKKLEERGYLRFSK-------TYVQLTEEGTEVFWSLLEEFDPTRNAVFKGSQPLYHLFGKFPEVAEmmCmIRHIYGDDFmEIFETSLT 169
                                    16   |    26        36        46        56        66     |  76        86       | -     | 106       116       126       136       146 || |  156    |  166   
                                        20-MSE                                              72-MSE                94     102                                           148-MSE      161-MSE    
                                                                                                                                                                        149-MSE                
                                                                                                                                                                          151-MSE

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: MarR-like transcriptional regulators (34)

Protein domain: Protease production regulatory protein Hpr (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d2fxaa1	A:6-167
1b	d2fxab_	B:
1c	d2fxac_	C:
1d	d2fxad_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Bacillus subtilis. Organism_taxid: 1423. (15)

1a	2fxaA00	A:6-167
1b	2fxaD00	D:7-169
1c	2fxaC00	C:8-167
1d	2fxaB00	B:8-187

(no "Pfam Domain" information available for 2FXA)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HPR_BACSU | P11065)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
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	2fxa
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 42)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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