2HYF - JenaLib

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Title :   THE STRUCTURE OF APO-MNTR FROM BACILLUS SUBTILIS, SELENOMETHIONINE DERIVATIVE

Authors :   A. Glasfeld

Date :   06 Aug 06 (Deposition) - 07 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Transcriptional Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Dewitt, J. I. Kliegman, J. D. Helmann, R. G. Brennan, D. L. Farrens, A. Glasfeld
The Conformations Of The Manganese Transport Regulator Of Bacillus Subtilis In Its Metal-Free State.
J. Mol. Biol. V. 365 1257 2007
PubMed-ID: 17118401 | Reference-DOI: 10.1016/J.JMB.2006.10.080
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR MNTR
	Chains	:	A, B, C, D
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	MANGANESE TRANSPORT REGULATOR

		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 (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MSE	-1	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:106 , TRP A:107 , ASN A:108 , LYS B:93	BINDING SITE FOR RESIDUE SO4 A 150
02	AC2	SOFTWARE	LYS A:93 , SER B:106 , TRP B:107 , ASN B:108	BINDING SITE FOR RESIDUE SO4 B 150
03	AC3	SOFTWARE	ARG B:24 , VAL B:25 , SER B:26	BINDING SITE FOR RESIDUE SO4 B 151
04	AC4	SOFTWARE	HIS B:35 , PRO B:36 , SER B:37 , SER C:106 , TRP C:107 , ASN C:108 , LYS D:93	BINDING SITE FOR RESIDUE SO4 C 150
05	AC5	SOFTWARE	VAL C:25 , TYR C:54 , LYS C:56 , TYR C:57 , HOH C:157	BINDING SITE FOR RESIDUE SO4 C 151
06	AC6	SOFTWARE	HIS C:35 , PRO C:36 , SER C:37 , LYS C:93 , SER D:106 , TRP D:107 , ASN D:108	BINDING SITE FOR RESIDUE SO4 D 150
07	AC7	SOFTWARE	HIS D:35 , PRO D:36 , SER D:37	BINDING SITE FOR RESIDUE SO4 D 151
08	AC8	SOFTWARE	THR A:63 , SER A:64 , ARG D:24 , VAL D:25 , SER D:26	BINDING SITE FOR RESIDUE SO4 A 151
09	AC9	SOFTWARE	VAL D:34 , HIS D:35 , SER D:38	BINDING SITE FOR RESIDUE SO4 D 152
10	BC1	SOFTWARE	VAL C:34 , HIS C:35 , SER C:38 , HOH C:159 , ARG D:72 , TYR D:75 , TRP D:107	BINDING SITE FOR RESIDUE EPE D 300

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

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

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

(no "PROSITE Motif" information available for 2HYF)

(no "Exon" information available for 2HYF)

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:134
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:134
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    
           MNTR_BACSU     3 TPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
               SCOP domains d2hyfa1 A:3-62 Manganese transport regulator MntR           d2hyfa2 A:63-136 Manganese transport regulator MntR                        SCOP domains
               CATH domains 2hyfA01 A:3-73 'winged helix' repressor DNA binding domain             2hyfA02 A:74-136 Diphtheria Toxin Repressor, domain 2           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hyf A   3 TPSmEDYIEQIYmLIEEKGYARVSDIAEALAVHPSSVTKmVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
                               |    12  |     22        32        42        52        62        72        82        92       102       112       122       132    
                               |       15-MSE                     42-MSE                                                                                          
                               6-MSE

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:132
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  
           MNTR_BACSU     3 TPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQ 134
               SCOP domains d2hyfb1 B:3-62 Manganese transport regulator MntR           d2hyfb2 B:63-134 Manganese transport regulator MntR                      SCOP domains
               CATH domains 2hyfB01 B:3-73 'winged helix' repressor DNA binding      domain        2hyfB02 B:74-134 Diphtheria Toxin Repressor, domain 2         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..ee-----..eehhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hyf B   3 TPSmEDYIEQIYmLIEEKGYARVSDIAEALAVHPSSVTKmVQKLDKDEYLI-----GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQ 134
                               |    12  |     22        32        42        52|     | 62        72        82        92       102       112       122       132  
                               6-MSE   15-MSE                     42-MSE     53    59

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           MNTR_BACSU     2 TTPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKKTE 138
               SCOP domains d2hyfc1 C:2-62 Manganese transport regulator MntR            d2hyfc2 C:63-138 Manganese transport regulator MntR                          SCOP domains
               CATH domains 2hyfC01 C:2-73 'winged helix' repressor DNA binding domain              2hyfC02 C:74-138 Diphtheria Toxin Repressor, domain 2             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hyf C   2 TTPSmEDYIEQIYmLIEEKGYARVSDIAEALAVHPSSVTKmVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKKTE 138
                                |   11   |    21        31        41|       51        61        71        81        91       101       111       121       131       
                                6-MSE   15-MSE                     42-MSE

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           MNTR_BACSU     2 TTPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKKTE 138
               SCOP domains d2hyfd1 D:2-62 Manganese transport regulator MntR            d2hyfd2 D:63-138 Manganese transport regulator MntR                          SCOP domains
               CATH domains 2hyfD01 D:2-73 'winged helix' repressor DNA binding domain              2hyfD02 D:74-138 Diphtheria Toxin Repressor, domain 2             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.......eehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hyf D   2 TTPSmEDYIEQIYmLIEEKGYARVSDIAEALAVHPSSVTKmVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKKTE 138
                                |   11   |    21        31        41|       51        61        71        81        91       101       111       121       131       
                                6-MSE   15-MSE                     42-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(

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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 (2)

1a	2hyfC01	C:2-73
1b	2hyfD01	D:2-73
1c	2hyfA01	A:3-73
1d	2hyfB01	B:3-73

Topology: Diphtheria Toxin Repressor; domain 2 (34)

Homologous Superfamily: Diphtheria Toxin Repressor, domain 2 (32)

Bacillus subtilis. Organism_taxid: 1423 (2)

2a	2hyfA02	A:74-136
2b	2hyfB02	B:74-134
2c	2hyfC02	C:74-138
2d	2hyfD02	D:74-138

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MNTR_BACSU | P54512)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0030026	cellular manganese ion homeostasis	Any process involved in the maintenance of an internal steady state of manganese ions at the level of a cell.
	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: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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	Cis Peptide Bonds
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	2hyf
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Description

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Ligands, Modified Residues, Ions (3, 22)

Sites (10, 10)

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