1HXD - JenaLib

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Title :   CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN

Authors :   K. Kwon, E. D. Streaker, S. Ruparelia, D. Beckett

Date :   12 Jan 01 (Deposition) - 30 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Ligase, Repressor, Biotin, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. H. Weaver, K. Kwon, D. Beckett, B. W. Matthews
Corepressor-Induced Organization And Assembly Of The Biotin Repressor: A Model For Allosteric Activation Of A Transcriptional Regulator.
Proc. Natl. Acad. Sci. Usa V. 98 6045 2001
PubMed-ID: 11353844 | Reference-DOI: 10.1073/PNAS.111128198
(for further references see the PDB file header)

Molecule 1 - BIRA BIFUNCTIONAL PROTEIN
	Chains	:	A, B
	EC Number	:	6.3.4.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	BIOTIN REPRESSOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BTN	2	Ligand/Ion	BIOTIN

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BTN	1	Ligand/Ion	BIOTIN

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BTN	1	Ligand/Ion	BIOTIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:89 , THR A:90 , ASN A:91 , GLN A:112 , ARG A:116 , GLY A:117 , ARG A:118 , TRP A:123 , LEU A:133 , SER A:134 , LYS A:183 , GLY A:186 , ILE A:187 , LEU A:188 , GLY A:204 , ALA A:205 , GLY A:206	BINDING SITE FOR RESIDUE BTN A 500
2	AC2	SOFTWARE	SER B:89 , THR B:90 , GLN B:112 , GLY B:115 , ARG B:116 , GLY B:117 , ARG B:118 , ARG B:121 , TRP B:123 , TYR B:132 , LYS B:183 , GLY B:186 , ILE B:187 , LEU B:188 , ALA B:205 , GLY B:206	BINDING SITE FOR RESIDUE BTN B 501

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

Asymmetric Unit

No.	Residues
1	Trp A:173	-	Pro A:174
2	Trp B:173	-	Pro B:174

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_BIRA_ECOLI_001 *	P	61	A	BIRA_ECOLI	---	---	A/B	P	61	A
2	UniProt	VAR_BIRA_ECOLI_002 *	K	70	E	BIRA_ECOLI	---	---	A/B	K	70	E
	* ID not provided by source

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_BIRA_ECOLI_001 *	P	61	A	BIRA_ECOLI	---	---	A	P	61	A
2	UniProt	VAR_BIRA_ECOLI_002 *	K	70	E	BIRA_ECOLI	---	---	A	K	70	E
	* ID not provided by source

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_BIRA_ECOLI_001 *	P	61	A	BIRA_ECOLI	---	---	B	P	61	A
2	UniProt	VAR_BIRA_ECOLI_002 *	K	70	E	BIRA_ECOLI	---	---	B	K	70	E
	* ID not provided by source

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	BIRA_ECOLI	66-254	2	A:66-254 B:66-254

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	BIRA_ECOLI	66-254	1	A:66-254 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	BIRA_ECOLI	66-254	1	- B:66-254

(no "Exon" information available for 1HXD)

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:305
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:314
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313    
           BIRA_ECOLI     4 NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
               SCOP domains d1hxda1 A:4-63 Biotin repressor, N-terminal domain          d1hxda3 A:64-270 Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain                                                                                                                     d1hxda2 A:271-317                               SCOP domains
               CATH domains 1hxdA01 A:4-64 'winged helix' repressor DNA binding domain   1hxdA02 A:65-270 Bira Bifunctional Protein; Domain 2                                                                                                                                                          1hxdA03 A:271-313                          ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh....eehhhhhhhh..hhhhhhhhhhhhhh.....eee...eee........hhhhhhhh.....eee.....hhhhhhhh.........eee......................eeeeeeeee......hhhhhhhhhhhhhhhhhhhh....eee...eeee..eeeeeeeeeee......eeeeeeeee....---------.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....eeeeee..eeeeeeeeeee...eeeee....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------A--------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------BPL_LPL_CATALYTIC  PDB: A:66-254 UniProt: 66-254                                                                                                                                             --------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hxd A   4 NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAM---------QGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       | -       223       233       243       253       263       273       283       293       303       313    
                                                                                                                                                                                                                                         211       221

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:314
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313    
           BIRA_ECOLI     4 NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
               SCOP domains d1hxdb1 B:4-63 Biotin repressor, N-terminal domain          d1hxdb3 B:64-270 Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain                                                                                                                     d1hxdb2 B:271-317                               SCOP domains
               CATH domains 1hxdB01 B:4-64 'winged helix' repressor DNA binding domain   1hxdB02 B:65-270 Bira Bifunctional Protein; Domain 2                                                                                                                                                          1hxdB03 B:271-313                          ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh....eee...eee........hhhhhhhh.....eeeeeee.hhhhhhhhhhhhh....eeeeeee....hhhhh.........eeeeeeeee......hhhhhhhhhhhhhhhhhhh.....eee...eeee..eeeeeeeeeee......eeeeeeeee....---------.............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeee..eeeeeeeeee.....eeeee..eeeee.....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------A--------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------BPL_LPL_CATALYTIC  PDB: B:66-254 UniProt: 66-254                                                                                                                                             --------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hxd B   4 NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAM---------QGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 317
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       | -       223       233       243       253       263       273       283       293       303       313    
                                                                                                                                                                                                                                         211       221

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 '\|'

(no "Pfam Domain" information available for 1HXD)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BIRA_ECOLI | P06709)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004077	biotin-[acetyl-CoA-carboxylase] ligase activity	Catalysis of the reaction: ATP + biotin + apo-(acetyl-CoA:carbon-dioxide ligase (ADP forming)) = AMP + diphosphate + (acetyl-CoA:carbon-dioxide ligase (ADP forming)).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009102	biotin biosynthetic process	The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0009305	protein biotinylation	The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid.
	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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	1hxd
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	6.3.4.15
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	BIRA_ECOLI \| P06709	:	1bia 1bib 1k67 2ewn 4wf2

1bia	BIRA BIFUNCTIONAL PROTEIN (ACTS AS BIOTIN OPERON REPRESSOR AND BIOTIN HOLOENZYME SYNTHETASE) (E.C.6.3.4.15)
1bib	BIRA BIFUNCTIONAL PROTEIN (ACTS AS BIOTIN OPERON REPRESSOR AND BIOTIN HOLOENZYME SYNTHETASE) (E.C. 6.3.4.15) COMPLEX WITH BIOTINYLATED LYSINE

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