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Asym./Biol. Unit (Jmol Viewer)

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Title :   BACILLUS SUBTILIS YABJ

Authors :   J. L. Smith, S. Sinha, P. Rappu, S. C. Lange, P. Mantsala, H. Zalkin

Date :   09 Jul 99 (Deposition) - 26 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Perchloric Acid Soluble Protein, Purine Regulation, Yjgf/Yer057C Family, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sinha, P. Rappu, S. C. Lange, P. Mantsala, H. Zalkin, J. L. Smith
Crystal Structure Of Bacillus Subtilis Yabj, A Purine Regulatory Protein And Member Of The Highly Conserved Yjgf Family.
Proc. Natl. Acad. Sci. Usa V. 96 13074 1999
PubMed-ID: 10557275 | Reference-DOI: 10.1073/PNAS.96.23.13074
(for further references see the PDB file header)

Molecule 1 - PURINE REGULATORY PROTEIN YABJ
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)/PLYSS
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	EMC	2	Ligand/Ion	ETHYL MERCURY ION
3	HG	1	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:78 , MET A:81 , PHE A:84 , CYS A:104 , VAL A:105	BINDING SITE FOR RESIDUE HG A 126
2	AC2	SOFTWARE	PHE B:84 , VAL B:87 , ARG B:102 , CYS B:104	BINDING SITE FOR RESIDUE EMC B 500
3	AC3	SOFTWARE	VAL C:76 , PHE C:84 , VAL C:87 , ASN C:88 , ARG C:102 , CYS C:104	BINDING SITE FOR RESIDUE EMC C 501
4	AC4	SOFTWARE	HIS A:9 , SER A:55 , ALA A:59 , HOH A:523 , HIS B:51 , HOH B:580 , HOH B:627	BINDING SITE FOR RESIDUE ACY B 502
5	AC5	SOFTWARE	GLN A:93 , TYR A:94 , HOH A:667	BINDING SITE FOR RESIDUE ACY A 503
6	AC6	SOFTWARE	THR B:2 , VAL B:23 , ASN B:24 , HOH B:550 , HOH B:588	BINDING SITE FOR RESIDUE ACY B 504
7	AC7	SOFTWARE	THR A:2 , VAL A:23 , ASN A:24 , HOH A:514 , HOH A:578	BINDING SITE FOR RESIDUE ACY A 505
8	AC8	SOFTWARE	LYS B:8 , HIS B:9 , PRO B:37 , HOH B:616	BINDING SITE FOR RESIDUE ACY B 506
9	AC9	SOFTWARE	ALA C:66 , SER C:67 , THR C:70 , HOH C:614	BINDING SITE FOR RESIDUE ACY C 507

(no "SS Bond" information available for 1QD9)

(no "Cis Peptide Bond" information available for 1QD9)

(no "SAP(SNP)/Variant" information available for 1QD9)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0076	PS01094	Uncharacterized protein family UPF0076 signature.	RIDA_BACSU	100-118	3	A:100-118 B:100-118 C:100-118

(no "Exon" information available for 1QD9)

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:124
 aligned with RIDA_BACSU | P37552 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           RIDA_BACSU     2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
               SCOP domains d1qd9a_ A: Purine regulatory protein YabJ                                                                                    SCOP domains
               CATH domains 1qd9A00 A:2-125  [code=3.30.1330.40, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.............eeeee..eeeee...............hhhhhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhh.....eeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qd9 A   2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with RIDA_BACSU | P37552 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           RIDA_BACSU     2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
               SCOP domains d1qd9b_ B: Purine regulatory protein YabJ                                                                                    SCOP domains
               CATH domains 1qd9B00 B:2-125  [code=3.30.1330.40, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.............eeeee..eeeee...............hhhhhhhhhhhhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhh.....eeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qd9 B   2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with RIDA_BACSU | P37552 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           RIDA_BACSU     2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
               SCOP domains d1qd9c_ C: Purine regulatory protein YabJ                                                                                    SCOP domains
               CATH domains 1qd9C00 C:2-125  [code=3.30.1330.40, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.............eeeee..eeeee...............hhhhhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhh.....eeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------UPF0076            ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qd9 C   2 TKAVHTKHAPAAIGPYSQGIIVNNMFYSSGQIPLTPSGEMVNGDIKEQTHQVFSNLKAVLEEAGASFETVVKATVFIADMEQFAEVNEVYGQYFDTHKPARSCVEVARLPKDALVEIEVIALVK 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: YjgF-like (45)

Family: YjgF/L-PSP (23)

Protein domain: Purine regulatory protein YabJ (2)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1qd9a_	A:
1b	d1qd9b_	B:
1c	d1qd9c_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.40, no name defined] (35)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	1qd9A00	A:2-125
1b	1qd9B00	B:2-125
1c	1qd9C00	C:2-125

(no "Pfam Domain" information available for 1QD9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (RIDA_BACSU | P37552)

molecular function
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0046360	2-oxobutyrate biosynthetic process	The chemical reactions and pathways resulting in the formation of 2-oxobutyrate, the anion of the organic acid 2-oxobutyric acid, which contains a ketone group on carbon 2.
	GO:0009082	branched-chain amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009097	isoleucine biosynthetic process	The chemical reactions and pathways resulting in the formation of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	GO:0009636	response to toxic substance	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 toxic stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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