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Asym./Biol. Unit (Jmol Viewer)

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Title :   SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION

Authors :   V. V. Lunin, M. Perbandt, C. H. Betzel, A. M. Mikhailov

Date :   21 Nov 00 (Deposition) - 06 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

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

Keywords :   Endonuclease, Hydrolase, Nuclease, Magnesium, Signal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. V. Shlyapnikov, V. V. Lunin, M. Perbandt, K. M. Polyakov, V. Y. Lunin, V. M. Levdikov, C. Betzel, A. M. Mikhailov
Atomic Structure Of The Serratia Marcescens Endonuclease At 1. 1 A Resolution And The Enzyme Reaction Mechanism.
Acta Crystallogr. , Sect. D V. 56 567 2000
PubMed-ID: 10771425 | Reference-DOI: 10.1107/S090744490000322X
(for further references see the PDB file header)

Molecule 1 - NUCLEASE SM2 ISOFORM
	Chains	:	A, B
	EC Number	:	3.1.30.2
	Engineered	:	YES
	Expression System	:	SERRATIA MARCESCENS
	Expression System Taxid	:	615
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Other Details	:	MG BINDING SITE AT RESIDUE 127

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:57 , ASN A:119 , HOH A:939 , HOH A:1136 , HOH A:1163 , HOH A:1246 , HOH A:1248	BINDING SITE FOR RESIDUE SO4 A 801
2	AC2	SOFTWARE	ASN A:20 , ARG B:57 , ARG B:87 , HIS B:89 , ASN B:119 , HOH B:948 , HOH B:1138 , HOH B:1139 , HOH B:1189 , HOH B:1216 , HOH B:1219	BINDING SITE FOR RESIDUE SO4 B 802
3	AC3	SOFTWARE	HOH A:914 , HOH A:938 , THR B:77 , GLY B:78 , ARG B:87 , HOH B:861 , HOH B:870 , HOH B:1107	BINDING SITE FOR RESIDUE SO4 B 803
4	AC4	SOFTWARE	ARG A:25 , LYS A:84 , TYR A:107 , HOH A:905 , HOH A:964 , HOH A:1153 , HOH A:1174 , HOH A:1233	BINDING SITE FOR RESIDUE SO4 A 804
5	AC5	SOFTWARE	ASN A:119 , HOH A:1163 , HOH A:1164 , HOH A:1246 , HOH A:1247 , HOH A:1248 , HOH A:1249 , HOH A:1250	BINDING SITE FOR RESIDUE MG A 810
6	AC6	SOFTWARE	ASN B:119 , HOH B:1216 , HOH B:1217 , HOH B:1218 , HOH B:1219 , HOH B:1220	BINDING SITE FOR RESIDUE MG B 811

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 1G8T)

(no "SAP(SNP)/Variant" information available for 1G8T)

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 1G8T)

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 d1g8ta_ A: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1g8tA00 A:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhh....eeeeehhhhhhhhhhhhhhhhhhh.......eeeeeeee...................eeeeeeee........eeeeeee.......hhhhh..hhhhhhhhhh.......hhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8t 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 d1g8tb_ B: Sm endonuclease                                                                                                                                                                                                                        SCOP domains
               CATH domains 1g8tB00 B:5-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...................eeeeeeee........eeeeeee.......hhhhh..hhhhhhhhhh.......hhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8t 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	d1g8ta_	A:
1b	d1g8tb_	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. (1)

1a	1g8tA00	A:5-245
1b	1g8tB00	B:5-245

(no "Pfam Domain" information available for 1G8T)

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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(no "Cis Peptide Bonds" information available for 1g8t)

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

1smn	EXTRACELLULAR ENDONUCLEASE FROM SERRATIA MARCESCENS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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