1JL3 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF B. SUBTILIS ARSC

Authors :   X. -D. Su, M. S. Bennett

Date :   15 Jul 01 (Deposition) - 24 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Alpha-Beta Fold, Ptp-Loop, Arsenate Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Bennett, Z. Guan, M. Laurberg, X. D. Su
Bacillus Subtilis Arsenate Reductase Is Structurally And Functionally Similar To Low Molecular Weight Protein Tyrosine Phosphatases.
Proc. Natl. Acad. Sci. Usa V. 98 13577 2001
PubMed-ID: 11698660 | Reference-DOI: 10.1073/PNAS.241397198
(for further references see the PDB file header)

Molecule 1 - ARSENATE REDUCTASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ARSC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:10 , GLY A:12 , ASN A:13 , SER A:14 , CYS A:15 , ARG A:16 , SER A:17 , HOH A:1014 , HOH A:1047	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	CYS B:10 , THR B:11 , GLY B:12 , ASN B:13 , SER B:14 , CYS B:15 , ARG B:16 , SER B:17 , HOH B:1012 , HOH B:1067	BINDING SITE FOR RESIDUE SO4 B 1002
3	AC3	SOFTWARE	CYS C:10 , THR C:11 , GLY C:12 , ASN C:13 , SER C:14 , CYS C:15 , ARG C:16 , SER C:17 , HOH C:1009 , HOH C:1036	BINDING SITE FOR RESIDUE SO4 C 1003
4	AC4	SOFTWARE	CYS D:10 , GLY D:12 , ASN D:13 , SER D:14 , CYS D:15 , ARG D:16 , SER D:17 , HOH D:1015 , HOH D:1056	BINDING SITE FOR RESIDUE SO4 D 1004

(no "SS Bond" information available for 1JL3)

(no "Cis Peptide Bond" information available for 1JL3)

(no "SAP(SNP)/Variant" information available for 1JL3)

(no "PROSITE Motif" information available for 1JL3)

(no "Exon" information available for 1JL3)

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:137
 aligned with ARSC_BACSU | P45947 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           ARSC_BACSU     3 NKIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
               SCOP domains d1jl3a_ A: Arsenate reductase ArsC                                                                                                        SCOP domains
               CATH domains 1jl3A00 A:3-139  [code=3.40.50.270, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh............hhhhhh...eeee.hhhhhhhh.......eeee....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl3 A   3 NKIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with ARSC_BACSU | P45947 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           ARSC_BACSU     3 NKIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
               SCOP domains d1jl3b_ B: Arsenate reductase ArsC                                                                                                        SCOP domains
               CATH domains 1jl3B00 B:3-139  [code=3.40.50.270, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh.............hhhhhh...eeee.hhhhhhhh.......eeee....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl3 B   3 NKIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with ARSC_BACSU | P45947 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      
           ARSC_BACSU     4 KIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
               SCOP domains d1jl3c_ C: Arsenate reduc  tase ArsC                                                                                                     SCOP domains
               CATH domains 1jl3C00 C:4-139  [code=3.  40.50.270, no name defined]                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhh--..eeeeee......hhhhhhhhhhh............hhhhhhhh.eeee..-------------.eeee....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl3 C   4 KIIYFLCTGNSCRSQMAEGWAKQYL--EWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLC-------------VKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
                                    13        23    |  |33        43        53        63        73        |-         -  |    103       113       123       133      
                                                   28 31                                                 82            96

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with ARSC_BACSU | P45947 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      
           ARSC_BACSU     4 KIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCGDAADKCPMTPPHVKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
               SCOP domains d1jl3d_ D: Arsenate reductase ArsC                                                                                                       SCOP domains
               CATH domains 1jl3D00 D:4-139  [code=3.40.50.270, no name defined]                                                                                     CATH domains
           Pfam domains (1) --LMWPc-1jl3D01 D:6-135                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) --LMWPc-1jl3D02 D:6-135                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) --LMWPc-1jl3D03 D:6-135                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) --LMWPc-1jl3D04 D:6-135                                                                                                             ---- Pfam domains (4)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhh............hhhhhhhh.eeeeee.------------.eeeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jl3 D   4 KIIYFLCTGNSCRSQMAEGWAKQYLGDEWKVYSAGIEAHGLNPNAVKAMKEVGIDISNQTSDIIDSDILNNADLVVTLCG------------VKREHWGFDDPARAQGTEEEKWAFFQRVRDEIGNRLKEFAETGK 139
                                    13        23        33        43        53        63        73        83         -  |    103       113       123       133      
                                                                                                          83           96

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: Phosphotyrosine protein phosphatases I-like (60)

Superfamily: Phosphotyrosine protein phosphatases I (50)

Family: Low-molecular-weight phosphotyrosine protein phosphatases (29)

Protein domain: Arsenate reductase ArsC (12)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1jl3a_	A:
1b	d1jl3b_	B:
1c	d1jl3c_	C:
1d	d1jl3d_	D:

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=3.40.50.270, no name defined] (36)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (1)

1a	1jl3A00	A:3-139
1b	1jl3B00	B:3-139
1c	1jl3D00	D:4-139
1d	1jl3C00	C:4-139

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: LMWPc] (24)

Family: LMWPc (24)

Bacillus subtilis (3)

1a	LMWPc-1jl3D01	D:6-135
1b	LMWPc-1jl3D02	D:6-135
1c	LMWPc-1jl3D03	D:6-135
1d	LMWPc-1jl3D04	D:6-135

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ARSC_BACSU | P45947)

molecular function
	GO:0030612	arsenate reductase (thioredoxin) activity	Catalysis of the reaction: arsenate + thioredoxin = arsenite + thioredoxin disulfide. Thioredoxin disulfide is also known as oxidized thioredoxin.
	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.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0046685	response to arsenic-containing 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 an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.

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