3F72 - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE STAPHYLOCOCCUS AUREUS PI258 CADC METAL BINDING SITE 2 MUTANT

Authors :   A. Kandegedara, S. Thiyagarajan, K. C. Kondapalli, T. L. Stemmler, B. P. Rosen

Date :   07 Nov 08 (Deposition) - 07 Apr 09 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Cadmium Repressor Protein, Zinc Binding Site, Dimerization Site 2 Mutant, Cadmium Resistance, Dna-Binding, Plasmid, Transcription, Transcription Regulation, Dna Binding Protein, Metal Binding Protein, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kandegedara, S. Thiyagarajan, K. C. Kondapalli, T. L. Stemmler, B. P. Rosen
Role Of Bound Zn(Ii) In The Cadc Cd(Ii)/Pb(Ii)/Zn(Ii)-Responsive Repressor.
J. Biol. Chem. V. 284 14958 2009
PubMed-ID: 19286656 | Reference-DOI: 10.1074/JBC.M809179200
(for further references see the PDB file header)

Molecule 1 - CADMIUM EFFLUX SYSTEM ACCESSORY PROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	NA	5	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:64 , ALA B:71 , HOH B:140	BINDING SITE FOR RESIDUE NA A 123
2	AC2	SOFTWARE	ARG A:44 , HIS A:75	BINDING SITE FOR RESIDUE NA A 124
3	AC3	SOFTWARE	GLU B:102 , ALA B:103 , HOH B:138	BINDING SITE FOR RESIDUE NA B 123
4	AC4	SOFTWARE	ARG B:44 , HIS B:75 , HIS B:76 , THR B:79	BINDING SITE FOR RESIDUE NA B 124
5	AC5	SOFTWARE	ARG F:44 , HIS F:75 , HIS F:76	BINDING SITE FOR RESIDUE NA F 123

(no "SS Bond" information available for 3F72)

Asymmetric Unit

No.	Residues
1	Leu E:24	-	Gln E:25

(no "SAP(SNP)/Variant" information available for 3F72)

Asymmetric Unit (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	6	A:24-116 B:24-117 C:24-116 D:24-115 E:24-117 F:24-117
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	6	A:58-76 B:58-76 C:58-76 D:58-76 E:58-76 F:58-76

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	2	A:24-116 B:24-117 - - - -
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	2	A:58-76 B:58-76 - - - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	2	- - C:24-116 D:24-115 - -
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	2	- - C:58-76 D:58-76 - -

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	2	- - - - E:24-117 F:24-117
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	2	- - - - E:58-76 F:58-76

(no "Exon" information available for 3F72)

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:107
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:108
                                    18        28        38        48        58        68        78        88        98       108        
           CADC_STAAU     9 IFCYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKK 116
               SCOP domains d3f72a_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.-....eeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------HTH_ARSR_2  PDB: A:24-116 UniProt: 24-119                                                     PROSITE (1)
                PROSITE (2) -------------------------------------------------HTH_ARSR_1         ---------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3f72 A   9 IFGYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK-GKLALYSLGGEAIRQIMMIALAHKK 116
                                    18        28        38        48        58        68        78        88 | |    98       108        
                                                                                                            90 |                        
                                                                                                              92

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:108
                                    19        29        39        49        59        69        79        89        99       109        
           CADC_STAAU    10 FCYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKE 117
               SCOP domains d3f72b_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------HTH_ARSR_2  PDB: B:24-117 UniProt: 24-119                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------------HTH_ARSR_1         ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3f72 B  10 FGYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGGEAIRQIMMIALAHKKE 117
                                    19        29        39        49        59        69        79        89        99       109

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:106
                                    20        30        40        50        60        70        80        90       100       110      
           CADC_STAAU    11 CYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKK 116
               SCOP domains d3f72c_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.---..eeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------HTH_ARSR_2  PDB: C:24-116 UniProt: 24-119                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------HTH_ARSR_1         ---------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3f72 C  11 GYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK---LALYSLGGEAIRQIMMIALAHKK 116
                                    20        30        40        50        60        70        80        90   |   100       110      
                                                                                                          90  94

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:106
                                    19        29        39        49        59        69        79        89        99       109      
           CADC_STAAU    10 FCYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHK 115
               SCOP domains d3f72d_ D: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee..------..ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------HTH_ARSR_2  PDB: D:24-115 UniProt: 24-119                                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------HTH_ARSR_1         --------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3f72 D  10 FGYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR------LYSLGGEAIRQIMMIALAHK 115
                                    19        29        39        49        59        69        79        89      | 99       109      
                                                                                                          89     96

Chain E from PDB  Type:PROTEIN  Length:101
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:107
                                    20        30        40        50        60        70        80        90       100       110       
           CADC_STAAU    11 CYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKE 117
               SCOP domains d3f72e_ E: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhhh..ee.------...ee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------HTH_ARSR_2  PDB: E:24-117 UniProt: 24-119                                                      PROSITE (1)
                PROSITE (2) -----------------------------------------------HTH_ARSR_1         ----------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3f72 E  11 GYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNF------ALYSLGGEAIRQIMMIALAHKKE 117
                                    20        30        40        50        60        70        80       | -    |  100       110       
                                                                                                        88     95

Chain F from PDB  Type:PROTEIN  Length:102
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:108
                                    19        29        39        49        59        69        79        89        99       109        
           CADC_STAAU    10 FCYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKE 117
               SCOP domains d3f72f_ F: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh..ee...------.ee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------HTH_ARSR_2  PDB: F:24-117 UniProt: 24-119                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------------HTH_ARSR_1         ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3f72 F  10 FGYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK------YSLGGEAIRQIMMIALAHKKE 117
                                    19        29        39        49        59        69        79        89|      |99       109        
                                                                                                           90     97

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: ArsR-like transcriptional regulators (13)

Protein domain: automated matches (4)

Staphylococcus aureus [TaxId: 1280] (3)

1a	d3f72a_	A:
1b	d3f72b_	B:
1c	d3f72c_	C:
1d	d3f72d_	D:
1e	d3f72e_	E:
1f	d3f72f_	F:

(no "CATH Domain" information available for 3F72)

(no "Pfam Domain" information available for 3F72)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (CADC_STAAU | P20047)

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:0046686	response to cadmium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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.

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	Cis Peptide Bonds
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	3f72
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	CADC_STAAU \| P20047	:	1u2w

1u2w	CRYSTAL STRUCTURE OF THE STAPHYLOCOCCUS AUREUS PI258 CADC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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