3DBI - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SUGAR-BINDING TRANSCRIPTIONAL REGULATOR (LACI FAMILY) FROM ESCHERICHIA COLI COMPLEXED WITH PHOSPHATE

Authors :   Y. Patskovsky, S. Ozyurt, J. Freeman, B. Wu, M. Maletic, J. Koss, S. R. Wa J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   01 Jun 08 (Deposition) - 01 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Structural Genomics, Sugar-Binding Transcriptional Regulator, Protein Structure Initiative, Psi-2, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Transcription Regulation, Transcription Regulator, Repressor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, S. Ozyurt, J. Freeman, B. Wu, M. Maletic, J. Koss, S. R. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Sugar-Binding Transcriptional Regulato (Laci Family) From Escherichia Coli Complexed With Phosphate.
To Be Published
PubMed: search

Molecule 1 - SUGAR-BINDING TRANSCRIPTIONAL REGULATOR, LACI FAMILY
	Atcc	:	8739
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Taxid	:	562
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Gene	:	LACI
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Synonym	:	CRYPTIC ASC OPERON REPRESSOR

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 31)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	27	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 21)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:74 , TYR A:126 , ARG A:128 , ARG A:151 , SER A:193 , PRO A:194 , THR A:195 , HOH A:364	BINDING SITE FOR RESIDUE PO4 A 339
2	AC2	SOFTWARE	HIS B:74 , TYR B:126 , ARG B:128 , ARG B:151 , SER B:193 , PRO B:194 , THR B:195	BINDING SITE FOR RESIDUE PO4 B 339
3	AC3	SOFTWARE	HIS C:74 , TYR C:126 , ARG C:128 , ARG C:151 , SER C:193 , PRO C:194 , THR C:195 , HOH C:381	BINDING SITE FOR RESIDUE PO4 C 339
4	AC4	SOFTWARE	HIS A:84 , ARG A:87 , GLU A:91 , GLN A:302	BINDING SITE FOR RESIDUE GOL A 340

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

Asymmetric Unit

No.	Residues
1	Val A:268	-	Pro A:269
2	Val A:287	-	Pro A:288
3	Pro A:336	-	Ser A:337
4	Val B:268	-	Pro B:269
5	Val B:287	-	Pro B:288
6	Val C:268	-	Pro C:269
7	Val C:287	-	Pro C:288

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

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

(no "Exon" information available for 3DBI)

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:278
 aligned with ASCG_ECOLI | P24242 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:278
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327        
           ASCG_ECOLI    58 STQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIAPS 335
               SCOP domains d3dbia_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --3dbiA01 A:62-163,A:295-324  [code=3.40.50.2300, no name defined]                                      3dbiA02 A:164-294,A:325-337  [code=3.40.50.2300, no name defined]                                                                  3dbiA01 A:62-163,A:295-324    3dbiA02       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eeeee....hhhhh....eeee.hhhhhhhhhhhhhhhhhhh...........eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbi A  60 STQTLGLVVTNTLYHGIYFSELLFHAARmAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAImIYPRFLSVDEIDDIIDAHSQPImVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSmDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEmLLERGAKFSALVASNDDmAIGAmKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEmIQEIIGRLIFmLDGGDFSPPKTFSGKLIRRDSLIAPS 337
                                    69        79        89        99       109       119    |  129       139       149       159       169       179       189 |     199       209       219       229     | 239       249   |   259       269       279       289       299|      309 |     319       329        
                                                       88-MSE                             124-MSE                147-MSE                                     191-MSE                                     235-MSE           253-MSE|                                       300-MSE    311-MSE                      
                                                                                                                                                                                                                                258-MSE

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with ASCG_ECOLI | P24242 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:278
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
           ASCG_ECOLI    57 KSTQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIAP 334
               SCOP domains d3dbib_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---3dbiB01 B:62-163,B:295-324  [code=3.40.50.2300, no name defined]                                      3dbiB02 B:164-294,B:325-336  [code=3.40.50.2300, no name defined]                                                                  3dbiB01 B:62-163,B:295-324    3dbiB02      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeee....hhhhh....eeee.hhhhhhhhhhhhhhhhhhh...........eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbi B  59 KSTQTLGLVVTNTLYHGIYFSELLFHAARmAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAImIYPRFLSVDEIDDIIDAHSQPImVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSmDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEmLLERGAKFSALVASNDDmAIGAmKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEmIQEIIGRLIFmLDGGDFSPPKTFSGKLIRRDSLIAP 336
                                    68        78        88        98       108       118     | 128       138       148       158       168       178       188  |    198       208       218       228      |238       248    |  258       268       278       288       298 |     308  |    318       328        
                                                        88-MSE                             124-MSE                147-MSE                                     191-MSE                                     235-MSE           253-MSE|                                       300-MSE    311-MSE                     
                                                                                                                                                                                                                                 258-MSE

Chain C from PDB  Type:PROTEIN  Length:277
 aligned with ASCG_ECOLI | P24242 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:277
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       
           ASCG_ECOLI    58 STQTLGLVVTNTLYHGIYFSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEMLLERGAKFSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLIAP 334
               SCOP domains d3dbic_ C: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --3dbiC01 C:62-163,C:295-324  [code=3.40.50.2300, no name defined]                                      3dbiC02 C:164-294,C:325-336  [code=3.40.50.2300, no name defined]                                                                  3dbiC01 C:62-163,C:295-324    3dbiC02      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeee......hhh.ee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eeeee....hhhhh....eeee.hhhhhhhhhhhhhhhhhhh...........eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbi C  60 STQTLGLVVTNTLYHGIYFSELLFHAARmAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAImIYPRFLSVDEIDDIIDAHSQPImVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSmDSPTSIERLAGYKDALAQHGIALNEKLIANGKWTPASGAEGVEmLLERGAKFSALVASNDDmAIGAmKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEmIQEIIGRLIFmLDGGDFSPPKTFSGKLIRRDSLIAP 336
                                    69        79        89        99       109       119    |  129       139       149       159       169       179       189 |     199       209       219       229     | 239       249   |   259       269       279       289       299|      309 |     319       329       
                                                       88-MSE                             124-MSE                147-MSE                                     191-MSE                                     235-MSE           253-MSE|                                       300-MSE    311-MSE                     
                                                                                                                                                                                                                                258-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 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)

Escherichia coli K-12 [TaxId: 83333] (3)

1a	d3dbia_	A:
1b	d3dbib_	B:
1c	d3dbic_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Escherichia coli k12. Organism_taxid: 83333. (1)

1a	3dbiA02	A:164-294,A:325-337
1b	3dbiB02	B:164-294,B:325-336
1c	3dbiC02	C:164-294,C:325-336
1d	3dbiA01	A:62-163,A:295-324
1e	3dbiB01	B:62-163,B:295-324
1f	3dbiC01	C:62-163,C:295-324

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ASCG_ECOLI | P24242)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:336 - Ser A:337	[ RasMol ]
		Val A:268 - Pro A:269	[ RasMol ]
		Val A:287 - Pro A:288	[ RasMol ]
		Val B:268 - Pro B:269	[ RasMol ]
		Val B:287 - Pro B:288	[ RasMol ]
		Val C:268 - Pro C:269	[ RasMol ]
		Val C:287 - Pro C:288	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3dbi
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ASCG_ECOLI \| P24242
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ASCG_ECOLI \| P24242
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ASCG_ECOLI \| P24242	:	3brq

(no "Related Entries Specified in the PDB File" available for 3DBI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 31)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 6)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File