4WOP - JenaLib

Title :   NUCLEOTIDE TRIPHOSPHATE PROMISCUITY IN MYCOBACTERIUM TUBERCULOSIS DETHIOBIOTIN SYNTHETASE

Authors :   W. Salaemae, M. Y. Yap, K. L. Wegener, G. W. Booker, M. C. J. Wilce, S. W. Po

Date :   16 Oct 14 (Deposition) - 08 Apr 15 (Release) - 27 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Biotin Protein Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Salaemae, M. Y. Yap, K. L. Wegener, G. W. Booker, M. C. Wilce, S. W. Polyak
Nucleotide Triphosphate Promiscuity In Mycobacterium Tuberculosis Dethiobiotin Synthetase.
Tuberculosis (Edinb) V. 95 259 2015
PubMed-ID: 25801336 | Reference-DOI: 10.1016/J.TUBE.2015.02.046

Compounds

Molecule 1 - ATP-DEPENDENT DETHIOBIOTIN SYNTHETASE BIOD
	Chains	:	A, B, C, D
	EC Number	:	6.3.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BIOD, MRA_1582
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	419947
	Strain	:	ATCC 25177 / H37RA
	Synonym	:	DTB SYNTHETASE,DTBS,DETHIOBIOTIN SYNTHASE

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (2, 8)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CTP	3	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CTP	1	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CTP	2	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , VAL A:13 , GLY A:14 , LYS A:15 , THR A:16 , VAL A:17 , ASP A:49 , GLU A:108 , GLY A:111 , GLY A:169 , PRO A:197 , GLY A:199 , ALA A:200 , ALA A:201 , HOH A:448 , HOH A:464 , HOH A:476 , HOH A:477	binding site for residue CTP A 301
2	AC2	SOFTWARE	LEU A:143 , GLY A:144 , THR A:145 , LEU A:146 , ASN A:147 , ALA B:73	binding site for residue SO4 A 302
3	AC3	SOFTWARE	ALA A:73 , VAL A:115 , LEU B:143 , GLY B:144 , THR B:145 , LEU B:146 , ASN B:147 , HOH B:434 , HOH B:450 , HOH B:457 , HOH B:504	binding site for residue SO4 B 301
4	AC4	SOFTWARE	GLY B:12 , VAL B:13 , GLY B:14 , LYS B:15 , THR B:16 , HOH B:480 , HOH B:494	binding site for residue SO4 B 302
5	AC5	SOFTWARE	GLY C:12 , VAL C:13 , GLY C:14 , LYS C:15 , THR C:16 , VAL C:17 , LYS C:37 , ASP C:49 , GLU C:108 , GLY C:111 , GLY C:169 , PRO C:197 , GLY C:199 , ALA C:200 , ALA C:201 , HOH C:438	binding site for residue CTP C 301
6	AC6	SOFTWARE	LEU C:143 , GLY C:144 , THR C:145 , LEU C:146 , ASN C:147 , ALA D:73	binding site for residue SO4 C 302
7	AC7	SOFTWARE	THR D:11 , GLY D:12 , VAL D:13 , GLY D:14 , LYS D:15 , THR D:16 , VAL D:17 , GLU D:108 , GLY D:111 , GLY D:169 , SER D:170 , LEU D:196 , PRO D:197 , ALA D:198 , ALA D:200 , ALA D:201 , HOH D:465	binding site for residue CTP D 301
8	AC8	SOFTWARE	ALA C:73 , LEU D:143 , GLY D:144 , THR D:145 , LEU D:146 , ASN D:147 , HOH D:414 , HOH D:423	binding site for residue SO4 D 302

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Asymmetric Unit

No.	Residues
1	Glu A:119	-	Pro A:120
2	Asp A:173	-	Pro A:174
3	Glu B:119	-	Pro B:120
4	Asp B:173	-	Pro B:174
5	Glu C:119	-	Pro C:120
6	Glu D:119	-	Pro D:120
7	Asp D:173	-	Pro D:174

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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
	(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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhh...eeeeeeeee.hhhhh.hhhhhhhhhhh..eeeeeee.....hhhhhhhhh.....hhhhhhhhhhhhh...eeeeee..............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeeeeeee....hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wop A   1 ATILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhh..eeeee..eee.hhhh.hhhhhhhhhhh..eee..eee....hhhhhhhhhh....hhhhhhhhhhhhh...eeeeeeeeee...eee...eehhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wop B   1 ATILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeeeee.hhhhh.hhhhhhhhhhh...eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhh...eeeeee..............hhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wop C   1 ATILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhh..eeeee..ee.......hhhhhhhhhhh..eee..ee.....hhhhhhhhhh....hhhhhhhhhhhhh...eeeeee.......eee...eehhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhh.eeeeee.hhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wop D   1 ATILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLV 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 16)

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	Cis Peptide Bonds
		Asp A:173 - Pro A:174	[ RasMol ]
		Asp B:173 - Pro B:174	[ RasMol ]
		Asp D:173 - Pro D:174	[ RasMol ]
		Glu A:119 - Pro A:120	[ RasMol ]
		Glu B:119 - Pro B:120	[ RasMol ]
		Glu C:119 - Pro C:120	[ RasMol ]
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Description