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Title :   MUTANT HUMAN RIBONUCLEASE 1 (T24L, Q28L, R31L, R32L)

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 :   1.70

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 19)

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:125 , GLU B:125	BINDING SITE FOR RESIDUE CD A 1001
02	AC2	SOFTWARE	CL A:2001 , CL A:2002 , HOH A:2090	BINDING SITE FOR RESIDUE CD A 1002
03	AC3	SOFTWARE	CL B:2003 , CL B:2004 , HOH B:2032	BINDING SITE FOR RESIDUE CD B 1003
04	AC4	SOFTWARE	ASP A:126 , CL A:2005 , CL A:2006	BINDING SITE FOR RESIDUE CD A 1004
05	AC5	SOFTWARE	GLU B:49 , HIS B:80 , CL B:2007 , CL B:2008 , HOH B:2129	BINDING SITE FOR RESIDUE CD B 1005
06	AC6	SOFTWARE	HIS A:119 , CL A:2009	BINDING SITE FOR RESIDUE CD A 1006
07	AC7	SOFTWARE	HIS B:119 , CL B:2010 , HOH B:2160 , HOH B:2195	BINDING SITE FOR RESIDUE CD B 1007
08	AC8	SOFTWARE	GLU A:49 , HIS A:80 , CL A:2011 , HOH A:2138 , HOH A:2140 , HOH A:2142	BINDING SITE FOR RESIDUE CD A 1008
09	AC9	SOFTWARE	ARG A:104 , SER A:123 , CD A:1002 , CL A:2002	BINDING SITE FOR RESIDUE CL A 2001
10	BC1	SOFTWARE	LYS A:102 , ARG A:104 , GLU A:125 , CD A:1002 , CL A:2001	BINDING SITE FOR RESIDUE CL A 2002
11	BC2	SOFTWARE	LYS B:102 , ARG B:104 , SER B:123 , CD B:1003 , CL B:2004	BINDING SITE FOR RESIDUE CL B 2003
12	BC3	SOFTWARE	LYS B:102 , ARG B:104 , GLU B:125 , CD B:1003 , CL B:2003	BINDING SITE FOR RESIDUE CL B 2004
13	BC4	SOFTWARE	ASP A:83 , LYS A:102 , ASP A:126 , CD A:1004	BINDING SITE FOR RESIDUE CL A 2005
14	BC5	SOFTWARE	LYS A:74 , VAL A:124 , CD A:1004 , HOH A:2108 , HOH A:2201	BINDING SITE FOR RESIDUE CL A 2006
15	BC6	SOFTWARE	SER A:77 , GLU B:49 , HIS B:80 , CD B:1005 , CL B:2008 , HOH B:2021 , HOH B:2108	BINDING SITE FOR RESIDUE CL B 2007
16	BC7	SOFTWARE	SER A:77 , HOH A:2094 , HOH A:2154 , HIS B:80 , CD B:1005 , CL B:2007	BINDING SITE FOR RESIDUE CL B 2008
17	BC8	SOFTWARE	HIS A:12 , HIS A:119 , PHE A:120 , CD A:1006 , HOH A:2087	BINDING SITE FOR RESIDUE CL A 2009
18	BC9	SOFTWARE	HIS B:12 , HIS B:119 , PHE B:120 , CD B:1007 , HOH B:2043 , HOH B:2141	BINDING SITE FOR RESIDUE CL B 2010
19	CC1	SOFTWARE	GLU A:49 , HIS A:80 , CD A:1008 , HOH A:2018 , HOH A:2129 , SER B:77	BINDING SITE FOR RESIDUE CL A 2011

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

Exons (1, 2)

Sequences/Alignments

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
	(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:128
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:128
                                    38        48        58        68        78        88        98       108       118       128       138       148        
          RNAS1_HUMAN    29 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST 156
               SCOP domains d2e0ma_ A: automated matches                                                                                                     SCOP domains
               CATH domains 2e0mA00 A:1-128 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:1-128 UniProt: 1-165 [INCOMPLETE]                                                                              Transcript 1
                 2e0m A   1 KESRAKKFQRQHMDSDSSPSSSSLYCNLMMLLRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with RNAS1_HUMAN | P07998 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:128
                                    38        48        58        68        78        88        98       108       118       128       138       148        
          RNAS1_HUMAN    29 KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST 156
               SCOP domains d2e0mb_ B: automated matches                                                                                                     SCOP domains
               CATH domains 2e0mB00 B:1-128 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: B:1-128 UniProt: 1-165 [INCOMPLETE]                                                                              Transcript 1
                 2e0m B   1 KESRAKKFQRQHMDSDSSPSSSSLYCNLMMLLRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

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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