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Title :   CRYSTAL STRUCTURE OF THE TRNA PROCESSING ENZYME RNASE PH T125A MUTANT FROM AQUIFEX AEOLICUS

Authors :   R. Ishii, O. Nureki, S. Yokoyama, Riken Structural Genomics/Proteo Initiative (Rsgi)

Date :   02 May 03 (Deposition) - 23 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Ishii, O. Nureki, S. Yokoyama
Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Aquifex Aeolicus
J. Biol. Chem. V. 278 32397 2003
PubMed-ID: 12746447 | Reference-DOI: 10.1074/JBC.M300639200

Molecule 1 - RIBONUCLEASE PH
	Chains	:	A
	EC Number	:	2.7.7.56
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	RNASE PH

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION
2	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:123 , GLY A:124 , ALA A:125 , ARG A:126 , HOH A:927 , HOH A:973	BINDING SITE FOR RESIDUE PO4 A 701
2	AC2	SOFTWARE	VAL A:102 , GLU A:103 , LEU A:104 , THR A:105 , LYS A:156	BINDING SITE FOR RESIDUE SO4 A 910
3	AC3	SOFTWARE	THR A:60 , ARG A:99	BINDING SITE FOR RESIDUE SO4 A 911

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBONUCLEASE_PH	PS01277	Ribonuclease PH signature.	RNPH_AQUAE	116-129	1	A:116-129

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBONUCLEASE_PH	PS01277	Ribonuclease PH signature.	RNPH_AQUAE	116-129	6	A:116-129

(no "Exon" information available for 1UDQ)

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
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Chain A from PDB  Type:PROTEIN  Length:254
 aligned with RNPH_AQUAE | O67069 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    
           RNPH_AQUAE     2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVIQDGKWERSELKEVSSTT 255
               SCOP domains d1udqa1 A:2-150 Ribonuclease PH, domain 1                                                                                                            d1udqa2 A:151-255 Ribonuclease PH, domain 2                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------RNase_PH-1udqA01 A:10-143                                                                                                             -------------RNase_PH_C-1udqA02 A:157-224                                        ------------------------------- Pfam domains
         Sec.struct. author ............eeeee.......eeeeeee..eeeeeeeeee...hhhhh.....eeeeeeee..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee..eeee..hhhhhhh..eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee....eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_P------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1udq A   2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVIQDGKWERSELKEVSSTT 255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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 '\|'

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: RNase_PH (9)

Aquifex aeolicus (3)

RNase_PH-1udqA01

A:10-143

Clan: no clan defined [family: RNase_PH_C] (9)

Family: RNase_PH_C (9)

Aquifex aeolicus (3)

RNase_PH_C-1udqA02

A:157-224

Asymmetric Unit(hide GO term definitions)

Chain A (RNPH_AQUAE | O67069)

molecular function
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0009022	tRNA nucleotidyltransferase activity	Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.
	GO:0004549	tRNA-specific ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in tRNA molecules.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0016075	rRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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	RNPH_AQUAE \| O67069	:	1udn 1udo 1uds

1udn	WILD TYPE STRUCTURE
1udo	R86A MUTANT
1uds	R126A MUTANT RELATED ID: TRT001000260.3 RELATED DB: TARGETDB

Description

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