1WXO - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF ARCHAEAL TRANS-EDITING PROTEIN ALAX IN COMPLEX WITH ZINC

Authors :   M. Sokabe, A. Okada, T. Nakashima, M. Yao, I. Tanaka

Date :   27 Jan 05 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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

Keywords :   Hydrolase, Trans-Editing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sokabe, A. Okada, M. Yao, T. Nakashima, I. Tanaka
Molecular Basis Of Alanine Discrimination In Editing Site
Proc. Natl. Acad. Sci. Usa V. 102 11669 2005
PubMed-ID: 16087889 | Reference-DOI: 10.1073/PNAS.0502119102

Molecule 1 - ALANYL-TRNA SYNTHETASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	BL21-CODONPLUS-(DE3)-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH0574
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	TRANS-EDITING PROTEIN ALAX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:9 , HIS A:13 , CYS A:116 , HIS A:120	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	HIS B:9 , HIS B:13 , CYS B:116 , HIS B:120	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	SOFTWARE	HIS C:9 , HIS C:13 , CYS C:116 , HIS C:120	BINDING SITE FOR RESIDUE ZN C 1003

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

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

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

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

(no "Exon" information available for 1WXO)

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:152
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
               SCOP domains d1wxoa_ A: Hypothetical protein PH0574                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo A   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELE 154
               SCOP domains d1wxob_ B: Hypothetical protein PH0574                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo B   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELE 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          ALAXS_PYRHO     1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
               SCOP domains d1wxoc_ C: Hypothetical protein PH0574                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC01 C:103-143               --------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC02 C:103-143               --------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------tRNA_SAD-1wxoC03 C:103-143               --------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh.eeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wxo C   1 MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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) (23004)

Fold: RRF/tRNA synthetase additional domain-like (47)

Superfamily: ThrRS/AlaRS common domain (14)

Family: AlaX-like (7)

Protein domain: Hypothetical protein PH0574 (4)

Pyrococcus horikoshii [TaxId: 53953] (4)

1a	d1wxoa_	A:
1b	d1wxob_	B:
1c	d1wxoc_	C:

(no "CATH Domain" information available for 1WXO)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: tRNA_SAD] (15)

Family: tRNA_SAD (15)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (7)

1a	tRNA_SAD-1wxoC01	C:103-143
1b	tRNA_SAD-1wxoC02	C:103-143
1c	tRNA_SAD-1wxoC03	C:103-143

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ALAXS_PYRHO | O58307)

molecular function
	GO:0002161	aminoacyl-tRNA editing activity	The hydrolysis of an incorrectly aminoacylated tRNA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wxo)

Biological Units
	Complete Structure
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		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	1wxo
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	ALAXS_PYRHO \| O58307
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	ALAXS_PYRHO \| O58307
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UniProtKB/Swiss-Prot
	ALAXS_PYRHO \| O58307	:	1v4p 1v7o 1wnu 3rfn 3rhu

1v7o	THE SAME PROTEIN IN APO-FORM
1wnu	THE SAME PROTEIN IN COMPLEX WITH L-SERINE AND ZINC

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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