2VQ9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RNASE ZF-3E

Authors :   K. Kazakou, D. E. Holloway, S. H. Prior, V. Subramanian, K. R. Acharya

Date :   12 Mar 08 (Deposition) - 17 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Nuclease, Evolution, Hydrolase, Zebrafish, Polymorphism, Endonuclease, Ribonucleases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kazakou, D. E. Holloway, S. H. Prior, V. Subramanian, K. R. Acharya
Ribonuclease A Homologues Of The Zebrafish: Polymorphism, Crystal Structures Of Two Representatives And Their Evolutionary Implications
J. Mol. Biol. V. 380 206 2008
PubMed-ID: 18508078 | Reference-DOI: 10.1016/J.JMB.2008.04.070

Molecule 1 - RNASE 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 23-149
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955
	Synonym	:	RNASE ZF-3E

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:16 , THR A:49 , HOH A:2082	BINDING SITE FOR RESIDUE CL A1128
2	AC2	SOFTWARE	GLU A:93 , ARG A:94 , ASN A:97 , HOH A:2044	BINDING SITE FOR RESIDUE CL A1129

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:87
2	A:44	-	A:98
3	A:62	-	A:113

Asymmetric/Biological Unit

No.	Residues
1	Gln A:69	-	Thr A:70
2	Thr A:70	-	Asp A:71
3	His A:95	-	Pro A:96

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RNSL3_DANRE_002 *	R	56	G	RNSL3_DANRE	---	---	A	R	34	G
2	UniProt	VAR_RNSL3_DANRE_003 *	D	93	E	RNSL3_DANRE	---	---	A	D	71	E
3	UniProt	VAR_RNSL3_DANRE_004 *	N	102	D	RNSL3_DANRE	---	---	A	D	80	D
4	UniProt	VAR_RNSL3_DANRE_005 *	G	137	S	RNSL3_DANRE	---	---	A	G	115	S
5	UniProt	VAR_RNSL3_DANRE_006 *	T	141	A	RNSL3_DANRE	---	---	A	A	119	A
6	UniProt	VAR_RNSL3_DANRE_007 *	K	145	R	RNSL3_DANRE	---	---	A	R	123	R
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNSL3_DANRE	66-72	1	A:44-50

(no "Exon" information available for 2VQ9)

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:123
 aligned with RNSL3_DANRE | A5HAK0 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:123
                                    36        46        56        66        76        86        96       106       116       126       136       146   
          RNSL3_DANRE    27 IRRRYEHFLTQHVYGGITEQTCDRVMRQRRITRFPTGNDCKEVNTFIQANGNHVRTVCTGGGTRQTDNRDLYMSNNQFTVITCTLRSGERHPNCRYRGKESSRKIVVACEGEWPTHYEKGVIV 149
               SCOP domains d2vq9a_ A: automated matches                                                                                                SCOP domains
               CATH domains 2vq9A00 A:5-127 P-30 Protein                                                                                                CATH domains
               Pfam domains RnaseA-2vq9A01 A:5-122                                                                                                ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhhhhhh.............eeeee..hhhhhhhhhh..eee......eeee...eeeeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------G------------------------------------E--------D----------------------------------S---A---R---- SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P----------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vq9 A   5 IRRRYEHFLTQHVYGGITEQTCDRVMRQRRITRFPTGNDCKEVNTFIQANGNHVRTVCTGGGTRQTDNRDLYMSNDQFTVITCTLRSGERHPNCRYRGKESSRKIVVACEGEWPAHYERGVIV 127
                                    14        24        34        44        54        64        74        84        94       104       114       124

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: RNase A-like (356)

Superfamily: RNase A-like (356)

Family: automated matches (9)

Protein domain: automated matches (9)

Zebrafish (Danio rerio) [TaxId: 7955] (5)

d2vq9a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: P-30 Protein (299)

Homologous Superfamily: P-30 Protein (299)

Zebrafish (Danio rerio) (2)

2vq9A00

A:5-127

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RnaseA] (125)

Family: RnaseA (125)

Danio rerio (Zebrafish) (Brachydanio rerio) (1)

RnaseA-2vq9A01

A:5-122

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNSL3_DANRE | A5HAK0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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		His A:95 - Pro A:96	[ RasMol ]
		Thr A:70 - Asp A:71	[ RasMol ]

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	2vq9
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Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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