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Title :   CRYSTAL STRUCTURE OF A LACI-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN FROM CORYNEBACTERIUM GLUTAMICUM

Authors :   K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   03 Apr 09 (Deposition) - 14 Apr 09 (Release) - 14 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Crystal Structure, Transcription, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11232C, Structural Genomics, New York Sgx Research Center For Structural Genomics, Dna- Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of A Laci-Family Transcriptional Regulatory Protein From Corynebacterium Glutamicum
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATORS (LACI-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3 (BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CG0210, CGL0170
	Organism Common	:	BREVIBACTERIUM FLAVUM
	Organism Scientific	:	CORYNEBACTERIUM GLUTAMICUM
	Organism Taxid	:	1718

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:270 , ASP A:287 , SER A:289 , HOH A:463 , HOH A:464 , HOH A:465	BINDING SITE FOR RESIDUE MG A 1
2	AC2	SOFTWARE	ASP B:270 , ASP B:287 , SER B:289 , HOH B:447 , HOH B:448 , HOH B:449	BINDING SITE FOR RESIDUE MG B 2

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

Asymmetric/Biological Unit

No.	Residues
1	Val A:260	-	Pro A:261
2	Val B:260	-	Pro B:261

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

(no "PROSITE Motif" information available for 3GYB)

(no "Exon" information available for 3GYB)

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
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Chain A from PDB  Type:PROTEIN  Length:261
 aligned with Q8NTY1_CORGL | Q8NTY1 from UniProtKB/TrEMBL  Length:331

    Alignment length:269
                                    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       321         
         Q8NTY1_CORGL    62 RTQLIAVLIDDYSNPWFIDLIQSLSDVLTPKGYRLSVIDSLTSQAGTDPITSALSMRPDGIIIAQDIPDFTVPDSLPPFVIAGTRITQASTHDSVANDDFRGAEIATKHLIDLGHTHIAHLRVGSGAGLRRFESFEATMRAHGLEPLSNDYLGPAVEHAGYTETLALLKEHPEVTAIFSSNDITAIGALGAARELGLRVPEDLSIIGYDNTPLAQTRLINLTTIDDNSIGVGYNAALLLLSMLDPEAPHPEIMHTLQPSLIERGTCAPR 330
               SCOP domains d3gyba_ A: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhh....eeeee...--------...eeee...........eeeehhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eeeee..hhhhhh......eee.hhhhhhhhhhhhhhhhhh..........ee..eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gyb A  62 RTQLIAVLIDDYSNPWFIDLIQSLSDVLTPKGYRLSVIDSLTSQAGTDPITSALSmRPDGIIIAQDI--------LPPFVIAGTRITQASTHDSVANDDFRGAEIATKHLIDLGHTHIAHLRVGSGAGLRRFESFEATmRAHGLEPLSNDYLGPAVEHAGYTETLALLKEHPEVTAIFSSNDITAIGALGAARELGLRVPEDLSIIGYDNTPLAQTRLINLTTIDDNSIGVGYNAALLLLSmLDPEAPHPEImHTLQPSLIERGTCAPR 330
                                    71        81        91       101       111     | 121      |  -     | 141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 |     311  |    321         
                                                                                 117-MSE    128      137                                                            200-MSE                                                                                                303-MSE    314-MSE

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with Q8NTY1_CORGL | Q8NTY1 from UniProtKB/TrEMBL  Length:331

    Alignment length:268
                                    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       322        
         Q8NTY1_CORGL    63 TQLIAVLIDDYSNPWFIDLIQSLSDVLTPKGYRLSVIDSLTSQAGTDPITSALSMRPDGIIIAQDIPDFTVPDSLPPFVIAGTRITQASTHDSVANDDFRGAEIATKHLIDLGHTHIAHLRVGSGAGLRRFESFEATMRAHGLEPLSNDYLGPAVEHAGYTETLALLKEHPEVTAIFSSNDITAIGALGAARELGLRVPEDLSIIGYDNTPLAQTRLINLTTIDDNSIGVGYNAALLLLSMLDPEAPHPEIMHTLQPSLIERGTCAPR 330
               SCOP domains d3gybb_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhh....eeeee.............---------------...eehhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eeeee..hhhhhh......eee.hhhhhhhhhhhhhhhhh-------....ee..eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gyb B  63 TQLIAVLIDDYSNPWFIDLIQSLSDVLTPKGYRLSVIDSLTSQAGTDPITSALSmRPDGIIIAQDIPDFTVPDSLP---------------DSVANDDFRGAEIATKHLIDLGHTHIAHLRVGSGAGLRRFESFEATmRAHGLEPLSNDYLGPAVEHAGYTETLALLKEHPEVTAIFSSNDITAIGALGAARELGLRVPEDLSIIGYDNTPLAQTRLINLTTIDDNSIGVGYNAALLLLSmL-------EImHTLQPSLIERGTCAPR 330
                                    72        82        92       102       112    |  122       132     |   -         - |     162       172       182       192       202       212       222       232       242       252       262       272       282       292       302||     312 |     322        
                                                                                117-MSE              138             154                                           200-MSE                                                                                                303-MSE  312 |                
                                                                                                                                                                                                                                                                           304       314-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: automated matches (65)

Protein domain: automated matches (65)

Corynebacterium glutamicum [TaxId: 1718] (2)

1a	d3gyba_	A:
1b	d3gybb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8NTY1_CORGL | Q8NTY1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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/Biological Unit
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	Cis Peptide Bonds
		Val A:260 - Pro A:261	[ RasMol ]
		Val B:260 - Pro B:261	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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