3ISP - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ARGP FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   X. Zhou, Z. Lou, F. Sheng, M. Bartlam, H. Wang, Z. Rao

Date :   27 Aug 09 (Deposition) - 16 Feb 10 (Release) - 16 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Rod Shaped Structure, Dna Binding Domain, Regulatory Domain, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhou, Z. Lou, S. Fu, A. Yang, H. Shen, Z. Li, Y. Feng, M. Bartlam, H. Wang, Z. Rao
Crystal Structure Of Argp From Mycobacterium Tuberculosis Confirms Two Distinct Conformations Of Full-Length Lysr Transcriptional Regulators And Reveals Its Function In Dna Binding And Transcriptional Regulation.
J. Mol. Biol. 2009
PubMed-ID: 20036253 | Reference-DOI: 10.1016/J.JMB.2009.12.033

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR RV1985C/MT2039
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-29B
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RV1985C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37V

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3ISP)

(no "Site" information available for 3ISP)

(no "SS Bond" information available for 3ISP)

Asymmetric Unit

No.	Residues
1	Gly A:118	-	Asp A:119
2	Asp B:7	-	Gly B:8
3	Lys B:57	-	Pro B:58

(no "SAP(SNP)/Variant" information available for 3ISP)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LYSR	PS50931	LysR-type HTH domain profile.	Y1985_MYCTO	6-62	2	A:6-62 B:6-62
1	HTH_LYSR	PS50931	LysR-type HTH domain profile.	Y1985_MYCTU	6-62	2	A:6-62 B:6-62

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LYSR	PS50931	LysR-type HTH domain profile.	Y1985_MYCTO	6-62	4	A:6-62 B:6-62
1	HTH_LYSR	PS50931	LysR-type HTH domain profile.	Y1985_MYCTU	6-62	4	A:6-62 B:6-62

(no "Exon" information available for 3ISP)

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:290
 aligned with Y1985_MYCTO | P9WMF4 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
          Y1985_MYCTO     5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRGQ 296
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...ee.....ee...hhhhhhhhhhhhhhhhhhh....--.....eeeeeeehhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeehhhhhhhhh.....................hhhhhhhhhhhh...........hhhhhhhhhhh....eeeehhhhhhhhhhh..ee.....eeeeeeeeee...hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LYSR  PDB: A:6-62 UniProt: 6-62                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isp A   5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMG--ASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRGQ 296
                                    14        24        34        44        54        64        74        84  |  |  94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
                                                                                                             87 90

Chain A from PDB  Type:PROTEIN  Length:290
 aligned with Y1985_MYCTU | P9WMF5 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
          Y1985_MYCTU     5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRGQ 296
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...ee.....ee...hhhhhhhhhhhhhhhhhhh....--.....eeeeeeehhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeehhhhhhhhh.....................hhhhhhhhhhhh...........hhhhhhhhhhh....eeeehhhhhhhhhhh..ee.....eeeeeeeeee...hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -HTH_LYSR  PDB: A:6-62 UniProt: 6-62                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isp A   5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMG--ASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRGQ 296
                                    14        24        34        44        54        64        74        84  |  |  94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
                                                                                                             87 90

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Y1985_MYCTO | P9WMF4 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:291
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294 
          Y1985_MYCTO     5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRG 295
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh------...eeeeeehhhhhh.hhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeehhhhhhhh--............eee..--------------------.eee.....hhhhhhhh....eeeehhhhhhhhhhh..ee.....eeeeeeeeee...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LYSR  PDB: B:6-62 UniProt: 6-62                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isp B   5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEM------KRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRH--DGFTAAAAAKAPSLAWN--------------------PTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRG 295
                                    14        24        34        44        54        64        74        84 |      94       104       114       124       134       144       154       164       174  |  | 184       194 |       -         -  |    224       234       244       254       264       274       284       294 
                                                                                                            86     93                                                                                 177  |             196                  217                                                                              
                                                                                                                                                                                                         180

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Y1985_MYCTU | P9WMF5 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:291
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294 
          Y1985_MYCTU     5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRHLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKAFRRAITRPTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRG 295
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh------...eeeeeehhhhhh.hhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeehhhhhhhh--............eee..--------------------.eee.....hhhhhhhh....eeeehhhhhhhhhhh..ee.....eeeeeeeeee...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -HTH_LYSR  PDB: B:6-62 UniProt: 6-62                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isp B   5 QLDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEM------KRTRITIAVNADSMATWFSAVFDGLGDVLLDVRIEDQDHSARLLREGVAMGAVTTERNPVPGCRVHPLGEMRYLPVASRPFVQRH--DGFTAAAAAKAPSLAWN--------------------PTHFVPTTEGFTAAARAGLGWGMFPEKLAASPLADGSFVRVCDIHLDVPLYWQCWKLDSPIIARITDTVRAAASGLYRG 295
                                    14        24        34        44        54        64        74        84 |      94       104       114       124       134       144       154       164       174  |  | 184       194 |       -         -  |    224       234       244       254       264       274       284       294 
                                                                                                            86     93                                                                                 177  |             196                  217                                                                              
                                                                                                                                                                                                         180

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 "SCOP Domain" information available for 3ISP)

(no "CATH Domain" information available for 3ISP)

(no "Pfam Domain" information available for 3ISP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y1985_MYCTU | P9WMF5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0001130	bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0008156	negative regulation of DNA replication	Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
	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.

Chain A,B (Y1985_MYCTO | P9WMF4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3isp)

	Sites
(no "Sites" information available for 3isp)

	Cis Peptide Bonds
		Asp B:7 - Gly B:8	[ RasMol ]
		Gly A:118 - Asp A:119	[ RasMol ]
		Lys B:57 - Pro B:58	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (8, 12)

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