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Asym./Biol. Unit

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Description

Title :   X-RAY STRUCTURE OF M23L ONCONASE AT 100K

Authors :   A. Merlino, L. Mazzarella, A. Carannante, A. Di Fiore, A. Di Donato, E. Notomista, F. Sica

Date :   15 Feb 05 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

Chains :   Asym./Biol. Unit : A

Keywords :   Crystal Structure, Small Conformational Changes, Onconase Thermal Stability, Ribonucleases, Antitumor Action, Dynamics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Merlino, L. Mazzarella, A. Carannante, A. Di Fiore, A. Di Donato, E. Notomista, F. Sica
The Importance Of Dynamic Effects On The Enzyme Activity: X-Ray Structure And Molecular Dynamics Of Onconase Mutants
J. Biol. Chem. V. 280 17953 2005
PubMed-ID: 15728177 | Reference-DOI: 10.1074/JBC.M501339200
(for further references see the PDB file header)

Compounds

Molecule 1 - P-30 PROTEIN
	Chains	:	A
	EC Number	:	3.1.27.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	NORTHERN LEOPARD FROG
	Organism Scientific	:	RANA PIPIENS
	Organism Taxid	:	8404
	Synonym	:	ONCONASE

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PCA A:1 , LYS A:9 , HIS A:10 , LYS A:55 , HIS A:97 , PHE A:98 , HOH A:550 , HOH A:591 , HOH A:595 , HOH A:640	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	TRP A:3 , LYS A:45 , HOH A:536 , HOH A:570 , HOH A:610	BINDING SITE FOR RESIDUE SO4 A 701
3	AC3	SOFTWARE	ARG A:40 , PRO A:41 , GLU A:42 , HOH A:610 , HOH A:642	BINDING SITE FOR RESIDUE SO4 A 901

SS Bonds (4, 4)

Asymmetric/Biological Unit

No.	Residues
1	A:19	-	A:68
2	A:30	-	A:75
3	A:48	-	A:90
4	A:87	-	A:104

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1YV4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1YV4)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNP30_LITPI	30-36	1	A:30-36

Exons (0, 0)

(no "Exon" information available for 1YV4)

Sequences/Alignments

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
	(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:104
 aligned with RNP30_LITPI | P22069 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
          RNP30_LITPI     1 QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
               SCOP domains d1yv4a_ A: Amphibian cytotoxic ribonuclease                                                              SCOP domains
               CATH domains -1yv4A00 A:2-104 P-30 Protein                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhee.....hhhhhh.........eeeeee.hhhhhhhhhh.....eeee....eeeeeeee......eeeeeeee.eeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------RNASE_P-------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1yv4 A   1 xDWLTFQKKHITNTRDVDCDNILSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVTCENQAPVHFVGVGSC 104
                            |       10        20        30        40        50        60        70        80        90       100    
                            |                                                                                                       
                            1-PCA

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

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: Ribonuclease A-like (347)

Protein domain: Amphibian cytotoxic ribonuclease (18)

Frog (Rana pipiens), P-30 [TaxId: 8404] (10)

d1yv4a_

CATH Domains (1, 1)

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)

Northern leopard frog (Rana pipiens) (11)

1yv4A00

A:2-104

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1YV4)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNP30_LITPI | P22069)

molecular function
	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.
biological process
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yv4)

Still Images

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	1yv4
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	3.1.27.-
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RNP30_LITPI \| P22069	:	1onc 1pu3 1yv6 1yv7 2gmk 2i5s 2kb6 2lt5 3fd7 3hg6 3phn 3snf 3u00 3u01

Related Entries Specified in the PDB File

1yv6	THE SAME PROTEIN(M23L) AT 298K
1yv7	THE SAME PROTEIN(C87S,DES103-104) AT 298K