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Description

Title :   MUTANT HUMAN RIBONUCLEASE 1 (V52L, D53L, N56L, F59L)

Authors :   H. Yamada, T. Tamada, M. Kosaka, R. Kuroki

Date :   10 Oct 06 (Deposition) - 28 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)
Biol. Unit 4: A (2x),B (2x)

Keywords :   Mutant Human Pancreatic Ribonuclease 1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yamada, T. Tamada, M. Kosaka, K. Miyata, S. Fujiki, M. Tano, M. Moriya, M. Yamanishi, E. Honjo, H. Tada, T. Ino, H. Yamaguchi, J. Futami, M. Seno, T. Nomoto, T. Hirata, M. Yoshimura, R. Kuroki
'Crystal Lattice Engineering, ' An Approach To Engineer Protein Crystal Contacts By Creating Intermolecular Symmetry: Crystallization And Structure Determination Of A Mutant Human Rnase 1 With A Hydrophobic Interface Of Leucines
Protein Sci. V. 16 1389 2007
PubMed-ID: 17586772 | Reference-DOI: 10.1110/PS.072851407

Compounds

Molecule 1 - RIBONUCLEASE
	Chains	:	A, B
	EC Number	:	3.1.27.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBO26
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RIBONUCLEASE 1, RNASE 1, RNASE A, RNASE UPI-1, RIB-1, HP- RNASE

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A	B
Biological Unit 4 (2x)	:	A (2x)	B (2x)

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 11)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 22)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	18	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 14)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	10	Ligand/Ion	SULFATE ION

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:80 , GLU A:103 , HIS B:105	BINDING SITE FOR RESIDUE SO4 A 2001
02	AC2	SOFTWARE	HOH A:2046 , HOH A:2074 , HOH A:2088 , SER B:3 , ARG B:4	BINDING SITE FOR RESIDUE SO4 A 2002
03	AC3	SOFTWARE	ASP A:83 , LYS A:102 , ARG A:104	BINDING SITE FOR RESIDUE SO4 A 2003
04	AC4	SOFTWARE	ARG A:10 , GLN A:11 , ASN A:34 , MET A:35 , ARG A:39 , HOH A:2087	BINDING SITE FOR RESIDUE SO4 A 2005
05	AC5	SOFTWARE	ARG A:4 , HOH A:2083 , THR B:24 , GLN B:28 , ARG B:31	BINDING SITE FOR RESIDUE SO4 A 2007
06	AC6	SOFTWARE	GLN B:11 , HIS B:12 , HIS B:119 , PHE B:120 , HOH B:2021	BINDING SITE FOR RESIDUE SO4 B 2004
07	AC7	SOFTWARE	ARG B:39 , PRO B:42 , HOH B:2078	BINDING SITE FOR RESIDUE SO4 B 2006
08	AC8	SOFTWARE	LYS B:6 , GLN B:9 , ASP B:16 , LEU B:51 , GLN B:55 , HOH B:2013 , HOH B:2026 , HOH B:2046 , HOH B:2049	BINDING SITE FOR RESIDUE SO4 B 2008
09	AC9	SOFTWARE	SER B:15 , PRO B:50 , LEU B:51 , LEU B:52 , HOH B:2024 , HOH B:2049	BINDING SITE FOR RESIDUE SO4 B 2009
10	BC1	SOFTWARE	LYS A:6 , MET A:29 , ARG A:33	BINDING SITE FOR RESIDUE GOL A 1001
11	BC2	SOFTWARE	ARG A:39 , PRO A:42 , ASN A:67 , HOH A:2017 , HOH A:2056 , HOH A:2094	BINDING SITE FOR RESIDUE GOL A 1002

SS Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	A:26	-	A:84
2	A:40	-	A:95
3	A:58	-	A:110
4	A:65	-	A:72
5	B:26	-	B:84
6	B:40	-	B:95
7	B:58	-	B:110
8	B:65	-	B:72

Cis Peptide Bonds (4, 4)

Asymmetric Unit

No.	Residues
1	Tyr A:92	-	Pro A:93
2	Ser A:113	-	Pro A:114
3	Tyr B:92	-	Pro B:93
4	Ser B:113	-	Pro B:114

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2E0O)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	2	A:40-46 B:40-46

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	1	A:40-46 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	1	- B:40-46

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	4	A:40-46 B:40-46

Biological Unit 4 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_PANCREATIC	PS00127	Pancreatic ribonuclease family signature.	RNAS1_HUMAN	68-74	4	A:40-46 B:40-46

Exons (1, 2)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000397970	1c	ENSE00001915577	chr14:21271007-21270956	52	RNAS1_HUMAN	-	0	0	-	-
1.2c	ENST00000397970	2c	ENSE00001530999	chr14:21270478-21270408	71	RNAS1_HUMAN	-	0	0	-	-
1.3a	ENST00000397970	3a	ENSE00001837426	chr14:21270252-21269542	711	RNAS1_HUMAN	1-165	165	2	A:1-126 B:0-124	126 125

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:126
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:126
                                    38        48        58        68        78        88        98       108       118       128       138       148      
          RNAS1_HUMAN    29 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 154
               SCOP domains d2e0oa_ A: automated matches                                                                                                   SCOP domains
               CATH domains 2e0oA00 A:1-126 P-30 Protein                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..........hhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------RNASE_P-------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3a  PDB: A:1-126 UniProt: 1-165 [INCOMPLETE]                                                                            Transcript 1
                 2e0o A   1 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLLLVQLVCLQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVED 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:125
                                    37        47        57        67        77        87        97       107       117       127       137       147     
          RNAS1_HUMAN    28 GKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASV 152
               SCOP domains d2e0ob_ B: automated matches                                                                                                  SCOP domains
               CATH domains 2e0oB00 B:0-124 P-30 Protein                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.........hhhhhhhhhhh.........eeeee..hhhhhhhhh..eee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------RNASE_P------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.3a  PDB: B:0-124 UniProt: 1-165 [INCOMPLETE]                                                                           Transcript 1
                 2e0o B   0 MKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLLLVQLVCLQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASV 124
                                     9        19        29        39        49        59        69        79        89        99       109       119

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, 2)

Asymmetric 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: automated matches (86)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d2e0oa_	A:
1b	d2e0ob_	B:

CATH Domains (1, 2)

Asymmetric 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)

Human (Homo sapiens) (46)

1a	2e0oB00	B:0-124
1b	2e0oA00	A:1-126

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2E0O)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RNAS1_HUMAN | P07998)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004522	ribonuclease A activity	Catalysis of the endonucleolytic cleavage of RNA to 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RNAS1_HUMAN \| P07998	:	1dza 1e21 1h8x 1z7x 2e0j 2e0l 2e0m 2k11 2q4g 3f8g 4kxh

Related Entries Specified in the PDB File

2e0j 2e0l 2e0m