2O3F - JenaLib

Title :   STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE PUTATIVE TRANSCRIPTIONAL REGULATOR YBBH FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168.

Authors :   K. Tan, L. Bigelow, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   01 Dec 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Apc85504, Putative Transcriptional Regulator Ybbh, Bacillus Subtilis Subsp. Subtilis Str. 168, Structural Genomics, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, L. Bigelow, J. Abdullah, A. Joachimiak
The Crystal Structure Of The N-Terminal Domain Of The Putative Transcriptional Regulator Ybbh From Bacillus Subtilis Subsp. Subtilis Str. 168.
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 38)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA C:29 , HIS C:30 , PRO C:31 , HIS C:32 , MLY C:33	BINDING SITE FOR RESIDUE SO4 C 201
02	AC2	SOFTWARE	HIS B:30 , PRO B:31 , HIS B:32 , MLY B:33 , HOH B:228 , HOH B:247 , MLY C:15	BINDING SITE FOR RESIDUE SO4 B 202
03	AC3	SOFTWARE	ALA A:29 , HIS A:30 , PRO A:31 , HIS A:32 , MLY A:33 , MLY B:15	BINDING SITE FOR RESIDUE SO4 A 203
04	AC4	SOFTWARE	SER B:49 , ARG B:55 , HOH B:244 , HOH B:249	BINDING SITE FOR RESIDUE SO4 B 204
05	AC5	SOFTWARE	SER C:49 , ALA C:51 , ALA C:52 , ARG C:55 , SO4 C:212 , HOH C:244 , HOH C:256	BINDING SITE FOR RESIDUE SO4 C 205
06	AC6	SOFTWARE	SER A:49 , ALA A:51 , ALA A:52 , ARG A:55 , HOH A:256	BINDING SITE FOR RESIDUE SO4 A 206
07	AC7	SOFTWARE	GLN B:10 , MLY B:13 , HIS B:14	BINDING SITE FOR RESIDUE SO4 B 207
08	AC8	SOFTWARE	GLN C:10 , MLY C:13 , HIS C:14	BINDING SITE FOR RESIDUE SO4 C 208
09	AC9	SOFTWARE	GLN A:10 , MLY A:13 , HIS A:14	BINDING SITE FOR RESIDUE SO4 A 209
10	BC1	SOFTWARE	PRO A:17 , PRO A:18 , SER A:19 , GLU A:20 , ARG A:55	BINDING SITE FOR RESIDUE SO4 A 210
11	BC2	SOFTWARE	PRO B:17 , PRO B:18 , SER B:19 , GLU B:20 , ARG B:55	BINDING SITE FOR RESIDUE SO4 B 211
12	BC3	SOFTWARE	PRO C:17 , PRO C:18 , SER C:19 , GLU C:20 , ARG C:55 , SO4 C:205	BINDING SITE FOR RESIDUE SO4 C 212
13	BC4	SOFTWARE	ILE C:54 , GLY C:64 , PHE C:65 , GLN C:66 , HOH C:225 , HOH C:240	BINDING SITE FOR RESIDUE SO4 C 213
14	BC5	SOFTWARE	GLY A:64 , PHE A:65 , GLN A:66 , HOH A:220 , HOH A:221	BINDING SITE FOR RESIDUE SO4 A 214
15	BC6	SOFTWARE	GLY B:64 , PHE B:65 , GLN B:66 , HOH B:238 , HOH B:250	BINDING SITE FOR RESIDUE SO4 B 215

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:83
 aligned with YBBH_BACSU | Q45581 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:83
                                    10        20        30        40        50        60        70        80   
            YBBH_BACSU    1 MATGGLAIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVAGDLAKPTFQG 83
               SCOP domains d2o3fa1 A:1-83 Putative transcriptional regulator YbbH                              SCOP domains
               CATH domains -2o3fA00 A:2-83 'winged helix' repressor DNA binding domain                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HTH_RPIR  PDB: A:3-79 UniProt: 3-79                                          ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2o3f A  1 mATGGLAIIQSmkHkLPPSERKLADYILAHPHkAIESTVNEISALANSSDAAVIRLCkSLGLKGFQDLkmRVAGDLAKPTFQG 83
                            |       10 || |   20        30  |     40        50       |60        70        80   
                            |         12-MSE               33-MLY                   58-MLY     69-MLY          
                            1-MSE      13-MLY                                                   70-MSE         
                                         15-MLY

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with YBBH_BACSU | Q45581 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:82
                                    11        21        31        41        51        61        71        81  
            YBBH_BACSU    2 ATGGLAIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVAGDLAKPTFQG 83
               SCOP domains d2o3fb_ B: Putative transcriptional regulator YbbH                                 SCOP domains
               CATH domains 2o3fB00 B:2-83 'winged helix' repressor DNA binding domain                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_RPIR  PDB: B:3-79 UniProt: 3-79                                          ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  2o3f B  2 ATGGLAIIQSmkHkLPPSERKLADYILAHPHkAIESTVNEISALANSSDAAVIRLCkSLGLKGFQDLkmRVAGDLAKPTFQG 83
                                    11|| |    21        31 |      41        51      | 61       |71        81  
                                     12-MSE               33-MLY                   58-MLY     69-MLY          
                                      13-MLY                                                   70-MSE         
                                        15-MLY

Chain C from PDB  Type:PROTEIN  Length:83
 aligned with YBBH_BACSU | Q45581 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:83
                                    10        20        30        40        50        60        70        80   
            YBBH_BACSU    1 MATGGLAIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVAGDLAKPTFQG 83
               SCOP domains d2o3fc_ C: Putative transcriptional regulator YbbH                                  SCOP domains
               CATH domains -2o3fC00 C:2-83 'winged helix' repressor DNA binding domain                         CATH domains
           Pfam domains (1) --HTH_6-2o3fC01 C:3-79                                                         ---- Pfam domains (1)
           Pfam domains (2) --HTH_6-2o3fC02 C:3-79                                                         ---- Pfam domains (2)
           Pfam domains (3) --HTH_6-2o3fC03 C:3-79                                                         ---- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HTH_RPIR  PDB: C:3-79 UniProt: 3-79                                          ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2o3f C  1 mATGGLAIIQSmkHkLPPSERKLADYILAHPHkAIESTVNEISALANSSDAAVIRLCkSLGLKGFQDLkmRVAGDLAKPTFQG 83
                            |       10 || |   20        30  |     40        50       |60        70        80   
                            1-MSE     12-MSE               33-MLY                   58-MLY     69-MLY          
                                       13-MLY                                                   70-MSE         
                                         15-MLY

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YBBH_BACSU | Q45581)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0004360	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate.
	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:0006047	UDP-N-acetylglucosamine metabolic process	The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006002	fructose 6-phosphate metabolic process	The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
	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.

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