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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ECOLI BIOTIN REPRESSOR WITH CO-REPRESSOR ANALOG

Authors :   Z. A. Wood, L. H. Weaver, B. W. Matthews

Date :   04 Nov 05 (Deposition) - 21 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Helix-Turn-Helix, Disorder-To-Order Transition, Biotin, Ligase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. A. Wood, L. H. Weaver, P. H. Brown, D. Beckett, B. W. Matthews
Co-Repressor Induced Order And Biotin Repressor Dimerization: A Case For Divergent Followed By Convergent Evolution.
J. Mol. Biol. V. 357 509 2006
PubMed-ID: 16438984 | Reference-DOI: 10.1016/J.JMB.2005.12.066
(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 Plasmid	:	PBTAC
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BIRA, BIOR, DHBB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	BIOTIN OPERON REPRESSOR, BIOTIN--[ACETYL-COA- CARBOXYLASE] SYNTHETASE, BIOTIN--PROTEIN LIGASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BTX	2	Ligand/Ion	((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYLHYDROGEN PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:89 , THR B:90 , ASN B:91 , GLN B:112 , GLY B:115 , ARG B:116 , GLY B:117 , ARG B:118 , ARG B:121 , LYS B:122 , TRP B:123 , PHE B:124 , ASP B:176 , LYS B:183 , GLY B:186 , ILE B:187 , ALA B:205 , GLY B:206 , ASN B:208 , VAL B:218 , ASN B:220 , GLN B:221 , TRP B:223 , GLU B:313	BINDING SITE FOR RESIDUE BTX B 500
2	AC2	SOFTWARE	SER A:89 , THR A:90 , GLN A:112 , GLY A:115 , ARG A:116 , GLY A:117 , ARG A:118 , ARG A:121 , LYS A:122 , TRP A:123 , PHE A:124 , ASP A:176 , GLY A:186 , ILE A:187 , LEU A:188 , ALA A:205 , GLY A:206 , ASN A:208 , VAL A:218 , ASN A:220 , GLN A:221 , TRP A:223 , HOH A:503 , HOH A:525	BINDING SITE FOR RESIDUE BTX A 501

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

Asymmetric/Biological Unit

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

Asymmetric/Biological 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)

Asymmetric/Biological 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

(no "Exon" information available for 2EWN)

Asymmetric/Biological 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:318
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:318
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        
           BIRA_ECOLI     3 DNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRSAE 320
               SCOP domains d2ewna1 A:3-63 Biotin repressor, N-terminal domain           d2ewna3 A:64-270 Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain                                                                                                                     d2ewna2 A:271-320                                  SCOP domains
               CATH domains 2ewnA01 A:3-64 'winged helix' repressor DNA binding domain    2ewnA02 A:65-270 Bira Bifunctional Protein; Domain 2                                                                                                                                                          2ewnA03 A:271-320                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh....eee...eee........hhhhhhh......eeeeeee.hhhhhhhh.........eeeeeee..................eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee.....eee..eeeeeeeeeeeee....eeeeeeeee..................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeeeee.....eeeee..eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------A--------E---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------BPL_LPL_CATALYTIC  PDB: A:66-254 UniProt: 66-254                                                                                                                                             ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ewn A   3 DNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRSAE 320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with BIRA_ECOLI | P06709 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       
           BIRA_ECOLI     2 KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRS 318
               SCOP domains d2ewnb1 B:2-63 Biotin repressor, N-terminal domain            d2ewnb3 B:64-270 Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain                                                                                                                     d2ewnb2 B:271-318                                SCOP domains
               CATH domains 2ewnB01 B:2-64 'winged helix' repressor DNA binding domain     2ewnB02 B:65-270 Bira Bifunctional Protein; Domain 2                                                                                                                                                          2ewnB03 B:271-318                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhh....eee...eee........hhhhhhh......eeeeeee.hhhhhhhhhhhhh....eeeeeee..................eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eee.....eee..eeeeeeeeeeeee....eeeeeeeee.................hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeeeeeeee.....eeee....eeee...eeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------A--------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------BPL_LPL_CATALYTIC  PDB: B:66-254 UniProt: 66-254                                                                                                                                             ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ewn B   2 KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQGPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRS 318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

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 2EWN)

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	2ewn
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	BIRA_ECOLI \| P06709	:	1bia 1bib 1hxd 1k67 4wf2

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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