2E7Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HIGH RESOLUTION STRUCTURE OF T. MARITIMA TRNASE Z

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

Date :   15 Jan 07 (Deposition) - 11 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

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

Keywords :   Rnase, Trna Maturation, Metallo-Beta-Lactamse, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Ishii, A. Minagawa, H. Takaku, M. Takagi, M. Nashimoto, S. Yokoyama
The Structure Of The Flexible Arm Of Thermotoga Maritima Trnase Z Differs From Those Of Homologous Enzymes
Acta Crystallogr. , Sect. F V. 63 637 2007
PubMed-ID: 17671357 | Reference-DOI: 10.1107/S1744309107033623
(for further references see the PDB file header)

Molecule 1 - TRNASE Z
	Chains	:	A, B
	EC Number	:	3.1.26.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	PGO	4	Ligand/Ion	S-1,2-PROPANEDIOL
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:52 , HIS A:53 , ASP A:190 , HIS A:244 , ZN A:1302 , HOH A:1416	BINDING SITE FOR RESIDUE ZN A 1301
02	AC2	SOFTWARE	HIS A:48 , HIS A:50 , HIS A:134 , ASP A:190 , ZN A:1301 , HOH A:1416	BINDING SITE FOR RESIDUE ZN A 1302
03	AC3	SOFTWARE	ALA A:120 , GLY A:121 , ARG A:149 , TYR A:180 , LYS A:182	BINDING SITE FOR RESIDUE SO4 A 501
04	AC4	SOFTWARE	LYS A:254 , ARG A:261 , TYR A:271 , HOH A:1305 , HOH A:1444	BINDING SITE FOR RESIDUE SO4 A 502
05	AC5	SOFTWARE	ASP B:52 , HIS B:53 , ASP B:190 , HIS B:244 , ZN B:2302 , HOH B:2373	BINDING SITE FOR RESIDUE ZN B 2301
06	AC6	SOFTWARE	HIS B:48 , HIS B:50 , ASP B:190 , ZN B:2301 , HOH B:2373	BINDING SITE FOR RESIDUE ZN B 2302
07	AC7	SOFTWARE	TRP A:14 , GLU A:28 , GLY A:29 , THR A:33 , THR B:32 , HOH B:2368	BINDING SITE FOR RESIDUE PGO A 601
08	AC8	SOFTWARE	ARG A:150 , GLU A:178 , GLU A:179 , HOH A:1354	BINDING SITE FOR RESIDUE PGO A 604
09	AC9	SOFTWARE	TRP B:14 , GLU B:28 , GLY B:29 , VAL B:30 , THR B:33 , HOH B:2368	BINDING SITE FOR RESIDUE PGO B 602
10	BC1	SOFTWARE	LYS B:254 , LYS B:258 , ARG B:261 , TYR B:271	BINDING SITE FOR RESIDUE PGO B 603

(no "SS Bond" information available for 2E7Y)

(no "Cis Peptide Bond" information available for 2E7Y)

(no "SAP(SNP)/Variant" information available for 2E7Y)

(no "PROSITE Motif" information available for 2E7Y)

(no "Exon" information available for 2E7Y)

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:272
 aligned with Q9WZW8_THEMA | Q9WZW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
         Q9WZW8_THEMA     1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
               SCOP domains d2e7ya_ A: Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee....eeeee..hhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee.....ee........eeeeeee.........eeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.......hhhhhh....eeee....--------...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh...eeee......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7y A   1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFL--------NHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 |       -|      230       240       250       260       270       280
                                                                                                                                                                                                                                             212      221

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with Q9WZW8_THEMA | Q9WZW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
         Q9WZW8_THEMA     1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRTKHVSSEVSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
               SCOP domains d2e7yb_ B: Ribonuclease Z (RNase Z)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee....eee....hhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhh-----...eeeeee..hhhhhhhhhhhhhhhhhhh..eeeeee.....ee........eeeeeee.------..eeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhheeeeeeeeeee.......hhhhhh...eeeee....hhhhh......hhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh...eeee......eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7y B   1 MNIIGFSKALFSTWIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNN-----EKPLDVFYPEGNRAVEEYTEFIKRANPDLRFSFNVHPLKEGERVFLRNAGGFKRYVQPFRT------VSFGYHIFEVRRKLKKEFQGLDSKEISRLVKEKGRDFVTEEYHKKVLTISGDSLALDPEEIRGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAGVKKVILYHISTRYIRQLKSVIKKYREEMPDVEILYMDPRKVFEM 280
                                    10        20        30        40        50        60     |   - |      80        90       100       110       120       130 |     140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
                                                                                            66    72                                                         132    139

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Metallo-hydrolase/oxidoreductase (184)

Superfamily: Metallo-hydrolase/oxidoreductase (184)

Family: RNase Z-like (5)

Protein domain: Ribonuclease Z (RNase Z) (5)

Thermotoga maritima [TaxId: 2336] (2)

1a	d2e7ya_	A:
1b	d2e7yb_	B:

(no "CATH Domain" information available for 2E7Y)

(no "Pfam Domain" information available for 2E7Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9WZW8_THEMA | Q9WZW8)

molecular function
	GO:0042781	3'-tRNA processing endoribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0034414	tRNA 3'-trailer cleavage, endonucleolytic	Endonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e7y)

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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