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Title :   CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 N71T MUTANT

Authors :   A. Suzuki, T. Numata, M. Yao, I. Tanaka, M. Kimura

Date :   14 Apr 03 (Deposition) - 29 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Alpha Plus Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Numata, A. Suzuki, Y. Kakuta, K. Kimura, M. Yao, I. Tanaka, Y. Yoshida, T. Ueda, M. Kimura
Crystal Structures Of The Ribonuclease Mc1 Mutants N71T And N71S In Complex With 5'-Gmp: Structural Basis For Alterations In Substrate Specificity
Biochemistry V. 42 5270 2003
PubMed-ID: 12731868 | Reference-DOI: 10.1021/BI034103G
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE MC
	Chains	:	A, B
	EC Number	:	3.1.27.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	BALSAM PEAR
	Organism Scientific	:	MOMORDICA CHARANTIA
	Organism Taxid	:	3673
	Synonym	:	RIBONUCLEASE MC1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:84 , LYS A:87 , HIS A:88 , HOH A:416 , HOH A:417 , HOH A:418 , HOH A:419 , HOH A:420	BINDING SITE FOR RESIDUE MN A 501
2	AC2	SOFTWARE	HIS B:34 , GLU B:84 , LYS B:87 , HIS B:88 , HOH B:421 , HOH B:422 , HOH B:423 , HOH B:424 , HOH B:425	BINDING SITE FOR RESIDUE MN B 503
3	AC3	SOFTWARE	ARG B:132 , HOH B:426 , HOH B:427 , HOH B:428 , HOH B:429 , HOH B:430	BINDING SITE FOR RESIDUE MN B 504

Asymmetric Unit

No.	Residues
1	A:15	-	A:23
2	A:48	-	A:91
3	A:151	-	A:184
4	A:168	-	A:179
5	B:15	-	B:23
6	B:48	-	B:91
7	B:151	-	B:184
8	B:168	-	B:179

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNMC_MOMCH	31-38	2	A:31-38 B:31-38
2	RNASE_T2_2	PS00531	Ribonuclease T2 family histidine active site 2.	RNMC_MOMCH	81-92	2	A:80-91 B:80-91

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNMC_MOMCH	31-38	1	A:31-38 -
2	RNASE_T2_2	PS00531	Ribonuclease T2 family histidine active site 2.	RNMC_MOMCH	81-92	1	A:80-91 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_T2_1	PS00530	Ribonuclease T2 family histidine active site 1.	RNMC_MOMCH	31-38	1	- B:31-38
2	RNASE_T2_2	PS00531	Ribonuclease T2 family histidine active site 2.	RNMC_MOMCH	81-92	1	- B:80-91

(no "Exon" information available for 1UCG)

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:190
 aligned with RNMC_MOMCH | P23540 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           RNMC_MOMCH     1 FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQGSGTSLTNCPQGSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 191
               SCOP domains d1ucga_ A: Ribonuclease MC1                                                                                                                                                                     SCOP domains
               CATH domains 1ucgA00 A:1-190 Ribonuclease Rh; Chain A                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhh.....hhhhh....eeeeeeeee..ee.....-....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhh...eeeeee......eeeeeeeeeee.....ee.........eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RNASE_T2------------------------------------------RNASE_T2_2  --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucg A   1 MDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLTNCP-GSPFDITKISHLQSQLNTLWPTVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 190
                                    10        20        30        40        |-|       59        69        79        89        99       109       119       129       139       149       159       169       179       189 
                                                                           49 |                                                                                                                                            
                                                                             50

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with RNMC_MOMCH | P23540 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           RNMC_MOMCH     1 FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQGSGTSLTNCPQGSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 191
               SCOP domains d1ucgb_ B: Ribonuclease MC1                                                                                                                                                                     SCOP domains
               CATH domains 1ucgB00 B:1-190 Ribonuclease Rh; Chain A                                                                                                                                                        CATH domains
           Pfam domains (1) -Ribonuclease_T2-1ucgB01 B:2-181                 -                                                                                                                                    --------- Pfam domains (1)
           Pfam domains (2) -Ribonuclease_T2-1ucgB02 B:2-181                 -                                                                                                                                    --------- Pfam domains (2)
         Sec.struct. author ..eeeeeeehhhhhhhh..............eeeeeeeee..ee.....-....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeehhhhhhhhhhhhh...eeeeee......eeeeeeeeeee.....ee.........eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RNASE_T2------------------------------------------RNASE_T2_2  --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ucg B   1 MDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLTNCP-GSPFDITKISHLQSQLNTLWPTVLRANNQQFWSHEWTKHGTCSESTFNQAAYFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 190
                                    10        20        30        40        |-|       59        69        79        89        99       109       119       129       139       149       159       169       179       189 
                                                                           49 |                                                                                                                                            
                                                                             50

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribonuclease Rh-like (20)

Superfamily: Ribonuclease Rh-like (20)

Family: Ribonuclease Rh-like (18)

Protein domain: Ribonuclease MC1 (8)

Bitter gourd (Momordica charantia) [TaxId: 3673] (8)

1a	d1ucga_	A:
1b	d1ucgb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Ribonuclease Rh; Chain A (18)

Homologous Superfamily: Ribonuclease Rh; Chain A (18)

Balsam pear (Momordica charantia) (8)

1a	1ucgA00	A:1-190
1b	1ucgB00	B:1-190

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribonuclease_T2] (11)

Family: Ribonuclease_T2 (11)

Momordica charantia (Bitter gourd) (Balsam pear) (4)

1a	Ribonuclease_T2-1ucgB01	B:2-181
1b	Ribonuclease_T2-1ucgB02	B:2-181

Asymmetric Unit(hide GO term definitions)

Chain A,B (RNMC_MOMCH | P23540)

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:0033897	ribonuclease T2 activity	Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides 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.

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	RNMC_MOMCH \| P23540	:	1bk7 1j1f 1j1g 1uca 1ucc 1ucd 1v9h

1bk7	WILD-TYPE ENZYME
1j1f	THE SAME MUTANT COMPLEXED WITH 5'-GMP
1j1g	N71S MUTANT COMPLEXED WITH 5'-GMP
1uca	WILD-TYPE ENZYME COMPLEXED WITH 2'-UMP
1ucc	WILD-TYPE ENZYME COMPLEXED WITH 3'-UMP
1ucd	WILD-TYPE ENZYME COMPLEXED WITH 5'-UMP

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Ligands, Modified Residues, Ions (1, 4)

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