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Title :   CRYSTAL STRUCTURE OF A PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YTCD

Authors :   M. Madegowda, S. Eswaramoorthy, K. Desigan, S. K. Burley, S. Swaminath York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   09 Aug 06 (Deposition) - 29 Aug 06 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna-Binding Protein, Hth-Type Transcription Regulators, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Madegowda, S. Eswaramoorthy, K. Desigan, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Hth-Type Transcription Regulator Ytcd
To Be Published
PubMed: search

Molecule 1 - PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YTCD
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 28)

No.	Name	Count	Type	Full Name
1	CSU	12	Mod. Amino Acid	CYSTEINE-S-SULFONIC ACID
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	CSU	6	Mod. Amino Acid	CYSTEINE-S-SULFONIC ACID
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	CSU	6	Mod. Amino Acid	CYSTEINE-S-SULFONIC ACID
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2HZT)

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

Asymmetric Unit

No.	Residues
1	Val A:66	-	Pro A:67
2	Val B:66	-	Pro B:67

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YTCD_BACSU	8-106	4	A:4-98 B:4-98 C:4-98 D:4-98

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YTCD_BACSU	8-106	2	A:4-98 B:4-98 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_HXLR	PS51118	HxlR-type HTH domain profile.	YTCD_BACSU	8-106	2	- - C:4-98 D:4-98

(no "Exon" information available for 2HZT)

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:98
 aligned with YTCD_BACSU | O34533 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           YTCD_BACSU     1 MEKKKYNISVEATLEVIGGKWKCVILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDMLCAWGANHINR 104
               SCOP domains ---------d2hzta1 A:4-98 Putative transcriptional regulator YtcD                                          SCOP domains
               CATH domains -2      hztA00 A:2-98 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_HXLR  PDB: A:4-98 UniProt: 8-106                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2hzt A   1 mS------LVEATLEVIGGKWKcVILcHLTHGKKRTSELKRLmPNITQKmLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDmLcAWGANHINR  98
                            ||      |4        14  |   | 24        34  |     44        54        64        74        84  | |   94    
                            ||      3            17-CSU              37-MSE 44-MSE                                     87-MSE       
                            1-MSE                    21-CSU                                                              89-CSU     
                             2

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with YTCD_BACSU | O34533 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           YTCD_BACSU     1 MEKKKYNISVEATLEVIGGKWKCVILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDMLCAWGANHINR 104
               SCOP domains d2      hztb_ B: automated matches                                                                       SCOP domains
               CATH domains -2      hztB00 B:2-98 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------hhhhhhhhhh..hhhhhhhhhhh..eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_HXLR  PDB: B:4-98 UniProt: 8-106                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2hzt B   1 mS------LVEATLEVIGGKWKcVILcHLTHGKKRTSELKRLmPNITQKmLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDmLcAWGANHINR  98
                            ||      |4        14  |   | 24        34  |     44        54        64        74        84  | |   94    
                            1-MSE   3            17-CSU              37-MSE 44-MSE                                     87-MSE       
                             2                       21-CSU                                                              89-CSU

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with YTCD_BACSU | O34533 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           YTCD_BACSU     1 MEKKKYNISVEATLEVIGGKWKCVILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDMLCAWGANHINR 104
               SCOP domains d2      hztc_ C: automated matches                                                                       SCOP domains
               CATH domains -2      hztC00 C:2-98 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------hhhhhhhhhh..hhhhhhhhhh...eehhhhhhhh...hhhhhhhhhhhhhhh..eeeee...---.eeeee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_HXLR  PDB: C:4-98 UniProt: 8-106                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2hzt C   1 mS------LVEATLEVIGGKWKcVILcHLTHGKKRTSELKRLmPNITQKmLTQQLRELEADGVINRIVYNQ---KVEYELSEYGRSLEGILDmLcAWGANHINR  98
                            ||      |4        14  |   | 24        34  |     44        54        64|   |   74        84  | |   94    
                            1-MSE   3            17-CSU              37-MSE 44-MSE               65  69                87-MSE       
                             2                       21-CSU                                                              89-CSU

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with YTCD_BACSU | O34533 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           YTCD_BACSU     1 MEKKKYNISVEATLEVIGGKWKCVILCHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEGILDMLCAWGANHINR 104
               SCOP domains d2      hztd_ D: automated matches                                                                       SCOP domains
               CATH domains -2      hztD00 D:2-98 'winged helix' repressor DNA binding domain                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------hhhhhhhhhh..hhhhhhhhhhh..eehhhhhhhh...hhhhhhhhhhhhhhh..eeeee...---.eeeee.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_HXLR  PDB: D:4-98 UniProt: 8-106                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2hzt D   1 mS------LVEATLEVIGGKWKcVILcHLTHGKKRTSELKRLmPNITQKmLTQQLRELEADGVINRIVYNQ---KVEYELSEYGRSLEGILDmLcAWGANHINR  98
                            ||      |4        14  |   | 24        34  |     44        54        64|   |   74        84  | |   94    
                            1-MSE   3            17-CSU              37-MSE 44-MSE               65  69                87-MSE       
                             2                       21-CSU                                                              89-CSU

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: automated matches (118)

Protein domain: automated matches (118)

Bacillus subtilis [TaxId: 1423] (6)

1a	d2hztb_	B:
1b	d2hztc_	C:
1c	d2hztd_	D:

Family: HxlR-like (6)

Protein domain: Putative transcriptional regulator YtcD (1)

Bacillus subtilis [TaxId: 1423] (1)

d2hzta1

A:4-98

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. (6)

1a	2hztC00	C:2-98
1b	2hztD00	D:2-98
1c	2hztA00	A:2-98
1d	2hztB00	B:2-98

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (YTCD_BACSU | O34533)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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.

Asymmetric Unit
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	Sites
(no "Sites" information available for 2hzt)

	Cis Peptide Bonds
		Val A:66 - Pro A:67	[ RasMol ]
		Val B:66 - Pro B:67	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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Description

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Ligands, Modified Residues, Ions (2, 28)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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