1ZKG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR, TETR FAMILY (TM1030) FROM THERMOTOGA MARITIMA AT 2.30 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   02 May 05 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tm1030, Transcriptional Regulator, Tetr Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Premkumar, C. L. Rife, S. Sri Krishna, D. Mcmullan, M. D. Miller, P. Abdubek, E. Ambing, T. Astakhova, H. L. Axelrod, J. M. Canaves, D. Carlton, H. J. Chiu, T. Clayton, M. Didonato, L. Duan, M. A. Elsliger J. Feuerhelm, R. Floyd, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, E. Koesema, J. S. Kovarik, A. Kreusch, I. Levin, T. M. Mcphillips, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, J. Paulsen, K. Quijano, R. Reyes, F. Rezezadeh, D. Rodionov, R. Schwarzenbacher, G. Spraggon, H. Van Den Bedem, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of Tm1030 From Thermotoga Maritima At 2. 3 A Resolution Reveals Molecular Details Of Its Transcription Repressor Function.
Proteins V. 68 418 2007
PubMed-ID: 17444523 | Reference-DOI: 10.1002/PROT.21436

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TM1030
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 16)

No.	Name	Count	Type	Full Name
1	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
2	UNL	2	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:85 , ILE A:86 , LYS A:89 , GLN A:125 , GLU A:162	BINDING SITE FOR RESIDUE UNL A 300
2	AC2	SOFTWARE	PHE B:66 , LYS B:89 , SER B:124 , VAL B:127 , PHE B:161	BINDING SITE FOR RESIDUE UNL B 300

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

(no "Cis Peptide Bond" information available for 1ZKG)

(no "SAP(SNP)/Variant" information available for 1ZKG)

(no "PROSITE Motif" information available for 1ZKG)

(no "Exon" information available for 1ZKG)

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:200
 aligned with Q9X0C0_THEMA | Q9X0C0 from UniProtKB/TrEMBL  Length:200

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
         Q9X0C0_THEMA     1 MLSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMTK 200
               SCOP domains -d1zkga1 A:2-75 Transcriptional regulator TM1030                           d1zkga2 A:76-200 Transcriptional regulator TM1030                                                                             SCOP domains
               CATH domains 1zkgA01 A:1-46 Homeodomain-like               1zkgA02 A:47-200 Tetracycline Repressor, domain 2                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zkg A   1 VLSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYmSVTEKLQKEFENFLmKNRNRDIFDFmERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLmWFFSGFEEVYLRTYQGKPELLKRDmNTLVEEVKVmLRILKKGmTK 200
                                    10        20        30        40        50     |  60        70|       80 |      90       100       110       120       130       140       150    |  160       170       180       190       200
                                                                                  56-MSE         71-MSE     82-MSE                                                                  155-MSE                  180-MSE   190-MSE 198-MSE

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with Q9X0C0_THEMA | Q9X0C0 from UniProtKB/TrEMBL  Length:200

    Alignment length:199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
         Q9X0C0_THEMA     2 LSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMTK 200
               SCOP domains d1zkgb1 B:2-75 Transcriptional regulator TM1030                           d1zkgb2 B:76-200 Transcriptional regulator TM1030                                                                             SCOP domains
               CATH domains 1zkgB01 B:2-46 Homeodomain-like              1zkgB02 B:47-200 Tetracycline Repressor, domain 2                                                                                                          CATH domains
           Pfam domains (1) ------TetR_N-1zkgB01 B:8-53                         --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------TetR_N-1zkgB02 B:8-53                         --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zkg B   2 LSKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYmSVTEKLQKEFENFLmKNRNRDIFDFmERWIEKKLEYSASHPEEADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLmWFFSGFEEVYLRTYQGKPELLKRDmNTLVEEVKVmLRILKKGmTK 200
                                    11        21        31        41        51    |   61        71        81|       91       101       111       121       131       141       151   |   161       171       181       191      |  
                                                                                 56-MSE         71-MSE     82-MSE                                                                  155-MSE                  180-MSE   190-MSE 198-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. (1)

1a	1zkgA01	A:1-46
1b	1zkgB01	B:2-46

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. (1)

2a	1zkgA02	A:47-200
2b	1zkgB02	B:47-200

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Thermotoga maritima (2)

1a	TetR_N-1zkgB01	B:8-53
1b	TetR_N-1zkgB02	B:8-53

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9X0C0_THEMA | Q9X0C0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (2, 2)

SS Bonds (0, 0)

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