3IWZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE C-DI-GMP RESPONSIVE GLOBAL REGULATOR CLP LINKS CELL-CELL SIGNALING TO VIRULENCE GENE EXPRESSION IN XANTHOMONAS CAMPESTRIS

Authors :   K. H. Chin, Z. L. Tu, Y. H. Tseng, J. M. Dow, A. H. J. Wang, S. H. Chou

Date :   03 Sep 09 (Deposition) - 15 Dec 09 (Release) - 09 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Xcc, Pathogenicity, Crp, Clp, C-Di-Gmp Receptor, Quorum Sensing, Dna- Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Chin, Y. C. Lee, Z. L. Tu, C. H. Chen, Y. H. Tseng, J. M. Yang, R. P. Ryan, Y. Mccarthy, J. M. Dow, A. H. Wang, S. H. Chou
The Camp Receptor-Like Protein Clp Is A Novel C-Di-Gmp Receptor Linking Cell-Cell Signaling To Virulence Gene Expression In Xanthomonas Campestris.
J. Mol. Biol. V. 396 646 2010
PubMed-ID: 20004667 | Reference-DOI: 10.1016/J.JMB.2009.11.076

Molecule 1 - CATABOLITE ACTIVATION-LIKE PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
	Organism Taxid	:	340
	Synonym	:	CAP-LIKE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3IWZ)

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

(no "Cis Peptide Bond" information available for 3IWZ)

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

Asymmetric Unit (3, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CLP_XANCP	22-122	3	A:22-122 B:22-122 D:22-122
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CLP_XANCP	158-230	4	A:158-228 B:158-228 C:158-229 D:158-229
3	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CLP_XANCP	188-211	4	A:188-211 B:188-211 C:188-211 D:188-211

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CLP_XANCP	22-122	2	A:22-122 - D:22-122
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CLP_XANCP	158-230	2	A:158-228 - - D:158-229
3	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CLP_XANCP	188-211	2	A:188-211 - - D:188-211

Biological Unit 2 (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CLP_XANCP	22-122	1	- B:22-122 -
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CLP_XANCP	158-230	2	- B:158-228 C:158-229 -
3	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CLP_XANCP	188-211	2	- B:188-211 C:188-211 -

(no "Exon" information available for 3IWZ)

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:207
 aligned with CLP_XANCP | P22260 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:207
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
            CLP_XANCP    22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYG 228
               SCOP domains d3iwza1 A:22-158 automated matches                                                                                                       d3iwza2 A:159-228 automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhh........eeee...eeeeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CNMP_BINDING_3  PDB: A:22-122 UniProt: 22-122                                                        -----------------------------------HTH_CRP_2  PDB: A:158-228 UniProt: 158-230                              PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:188-21----------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwz A  22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYG 228
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with CLP_XANCP | P22260 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:207
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
            CLP_XANCP    22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYG 228
               SCOP domains d3iwzb1 B:22-158 automated matches                                                                                                       d3iwzb2 B:159-228 automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh.......eeee...eeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee..hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CNMP_BINDING_3  PDB: B:22-122 UniProt: 22-122                                                        -----------------------------------HTH_CRP_2  PDB: B:158-228 UniProt: 158-230                              PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:188-21----------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwz B  22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYG 228
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with CLP_XANCP | P22260 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:207
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       
            CLP_XANCP    23 DAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYGT 229
               SCOP domains d3iwzc1 C:23-158 automated matches                                                                                                      d3iwzc2 C:159-229 automated matches                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhh........eeee...eeeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhh.hhhhhhhhhhhhhh.....ee..ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CNMP_BINDING_3  PDB: - UniProt: 22-122                                                              -----------------------------------HTH_CRP_2  PDB: C:158-229 UniProt: 158-230                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: C:188-21------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwz C  23 DAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYGT 229
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain D from PDB  Type:PROTEIN  Length:208
 aligned with CLP_XANCP | P22260 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:208
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
            CLP_XANCP    22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYGT 229
               SCOP domains d3iwzd1 D:22-158 automated matches                                                                                                       d3iwzd2 D:159-229 automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhh........eeee...eeeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eeee..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CNMP_BINDING_3  PDB: D:22-122 UniProt: 22-122                                                        -----------------------------------HTH_CRP_2  PDB: D:158-229 UniProt: 158-230                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: D:188-21------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwz D  22 LDAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVISGSVSIIAEEDDDRELVLGYFGSGEFVGEMGLFIESDTREVILRTRTQCELAEISYERLQQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHARGKTVVLYGT 229
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: automated matches (118)

Protein domain: automated matches (118)

Xanthomonas campestris [TaxId: 340] (1)

1a	d3iwza2	A:159-228
1b	d3iwzb2	B:159-228
1c	d3iwzc2	C:159-229
1d	d3iwzd2	D:159-229

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: automated matches (17)

Protein domain: automated matches (17)

Xanthomonas campestris [TaxId: 340] (1)

2a	d3iwza1	A:22-158
2b	d3iwzb1	B:22-158
2c	d3iwzc1	C:23-158
2d	d3iwzd1	D:22-158

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CLP_XANCP | P22260)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0035438	cyclic-di-GMP binding	Interacting selectively and non-covalently with cyclic-di-GMP, cyclic dimeric guanosine monophosphate.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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Biological Units
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	3iwz
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Ligands, Modified Residues, Ions (0, 0)

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