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Asym./Biol. Unit (Jmol Viewer)

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

Title :   IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS

Authors :   M. D. Miller, K. L. Krause

Date :   25 Jan 95 (Deposition) - 29 Jan 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nuclease, Dnase, Rnase, Sugar-Nonspecific Nuclease, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Miller, K. L. Krause
Identification Of The Serratia Endonuclease Dimer: Structural Basis And Implications For Catalysis.
Protein Sci. V. 5 24 1996
PubMed-ID: 8771193
(for further references see the PDB file header)

Molecule 1 - EXTRACELLULAR ENDONUCLEASE
	Chains	:	A, B
	EC Number	:	3.1.30.2
	Engineered	:	YES
	Expression System	:	SERRATIA MARCESCENS
	Expression System Gene	:	NUCA
	Expression System Plasmid	:	PUC19NUC4OC
	Expression System Taxid	:	615
	Expression System Vector Type	:	PLASMID
	Gene	:	NUCA
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Strain	:	SM6

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1SMN)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	ASA	AUTHOR	HIS A:89 , GLU A:127	PUTATIVE ACTIVE SITE REGION IN MONOMER A
2	ASB	AUTHOR	HIS B:89 , GLU B:127	PUTATIVE ACTIVE SITE REGION IN MONOMER B
3	INT	AUTHOR	ARG A:136 , ASP A:138 , ASN A:178 , PRO A:180 , ALA A:181 , VAL A:182 , ASN A:183 , HIS A:184 , ASP A:225 , SER A:229 , LYS A:233 , VAL A:236 , GLU A:239 , LEU A:240 , ASN A:245 , ARG B:136 , ASP B:138 , ASN B:178 , PRO B:180 , ALA B:181 , VAL B:182 , ASN B:183 , HIS B:184 , ASP B:225 , SER B:229 , LYS B:233 , VAL B:236 , GLU B:239 , LEU B:240 , ASN B:245 , HOH B:248 , HOH A:248 , HOH B:260 , HOH B:294 , HOH B:296 , HOH A:309 , HOH A:311	RESIDUES IN THE PHYSIOLOGICAL DIMER INTERFACE

Asymmetric/Biological Unit

No.	Residues
1	A:9	-	A:13
2	A:201	-	A:243
3	B:9	-	B:13
4	B:201	-	B:243

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUCLEASE_NON_SPEC	PS01070	DNA/RNA non-specific endonucleases active site.	NUCA_SERMA	107-115	2	A:86-94 B:86-94

(no "Exon" information available for 1SMN)

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:241
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:241
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265 
           NUCA_SERMA    26 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1smna_ A: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1smnA00 A:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....eeee..eeeeee....eeeeeeeeee.....................................................hhhhhhh........hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee..................eeeeeeeeee......eeeeeeeee..............hhhhhhhhheee.....hhhhhhhh....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smn A   5 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:241
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265 
           NUCA_SERMA    26 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1smnb_ B: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1smnB00 B:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
           Pfam domains (1) -------------------Endonuclease_NS-1smnB01 B:24-225                                                                                                                                                                          -------------------- Pfam domains (1)
           Pfam domains (2) -------------------Endonuclease_NS-1smnB02 B:24-225                                                                                                                                                                          -------------------- Pfam domains (2)
         Sec.struct. author .........eee.....eeee..eeeeee....eeeeeeeeee.....................................................hhhhhhh........hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee..................eeeeeeeeee......eeeeeeeee..............hhhhhhhhheee.....hhhhhhhh....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1smn B   5 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

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: His-Me finger endonucleases (64)

Superfamily: His-Me finger endonucleases (64)

Family: DNA/RNA non-specific endonuclease (7)

Protein domain: Sm endonuclease (5)

Serratia marcescens [TaxId: 615] (5)

1a	d1smna_	A:
1b	d1smnb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Extracellular Endonuclease; Chain A (4)

Homologous Superfamily: Extracellular Endonuclease, subunit A (4)

Serratia marcescens. Organism_taxid: 615. Strain: sm6. (2)

1a	1smnA00	A:5-245
1b	1smnB00	B:5-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: His-Me_finger (38)

Family: Endonuclease_NS (14)

Serratia marcescens (3)

1a	Endonuclease_NS-1smnB01	B:24-225
1b	Endonuclease_NS-1smnB02	B:24-225

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NUCA_SERMA | P13717)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
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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	Ligands, Modified Residues, Ions
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	Sites
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		ASB	[ RasMol ]	+environment [ RasMol ]
		INT	[ RasMol ]	+environment [ RasMol ]

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

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	1smn
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	3.1.30.2
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	NUCA_SERMA \| P13717	:	1g8t 1qae 1ql0 4e3y

(no "Related Entries Specified in the PDB File" available for 1SMN)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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