4E3Y - JenaLib

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Title :   X-RAY STRUCTURE OF THE SERRATIA MARCESCENS ENDONUCLEASE AT 0.95 A RESOLUTION

Authors :   A. A. Lashkov, V. V. Balaev, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikhai

Date :   11 Mar 12 (Deposition) - 08 May 13 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.95

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

Keywords :   Rossmann Fold, Hydrolase, Nucleic Acid, Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Lashkov, V. V. Balaev, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikhailov
X-Ray Structure Of The Serratia Marcescens Endonuclease At 0. 95 A Resolution
To Be Published
PubMed: search

Molecule 1 - NUCLEASE
	Chains	:	A, B
	EC Number	:	3.1.30.2
	Fragment	:	UNP RESIDUES 22-266
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Strain	:	SM6
	Synonym	:	ENDONUCLEASE, NUCLEASE ISOFORM SM2, NUCLEASE ISOFORM SM3, NUCLEASE ISOFORM SM1

		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 (5, 8)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:1119 , HOH A:2701 , HOH A:2702 , HOH A:2703 , HOH A:2704 , HOH A:2705	BINDING SITE FOR RESIDUE MG A 2601
2	AC2	SOFTWARE	ALA A:1169 , ASP A:1191 , ARG A:1213 , HOH A:2729 , ASP B:2208 , LYS B:2212	BINDING SITE FOR RESIDUE EDO A 2602
3	AC3	SOFTWARE	THR A:1035 , LYS A:1037 , LYS A:1162 , ALA A:1163 , HOH A:2781 , HOH A:2782 , HOH A:2979 , HOH A:3023	BINDING SITE FOR RESIDUE PEG A 2603
4	AC4	SOFTWARE	ASN B:2119 , HOH B:2401 , HOH B:2402 , HOH B:2403 , HOH B:2404 , HOH B:2405	BINDING SITE FOR RESIDUE MG B 2301
5	AC5	SOFTWARE	ASN A:1020 , GLY B:2054 , ARG B:2057 , ALA B:2094 , HOH B:2475 , HOH B:2592 , HOH B:2593 , HOH B:2630 , HOH B:2684	BINDING SITE FOR RESIDUE SO4 B 2302
6	AC6	SOFTWARE	ASN A:1020 , ARG B:2057 , ARG B:2087 , HIS B:2089 , ASN B:2119 , HOH B:2401 , HOH B:2402 , HOH B:2572 , HOH B:2712 , HOH B:2735	BINDING SITE FOR RESIDUE SO4 B 2303
7	AC7	SOFTWARE	THR B:2077 , GLY B:2078 , ARG B:2087 , HOH B:2517 , HOH B:2704	BINDING SITE FOR RESIDUE GOL B 2304
8	AC8	SOFTWARE	PRO B:2051 , ARG B:2131 , ILE B:2134 , ASP B:2135	BINDING SITE FOR RESIDUE EDO B 2305

Asymmetric Unit

No.	Residues
1	A:1009	-	A:1013
2	A:1201	-	A:1243
3	B:2009	-	B:2013
4	B:2201	-	B:2243

(no "Cis Peptide Bond" information available for 4E3Y)

(no "SAP(SNP)/Variant" information available for 4E3Y)

Asymmetric 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:1086-1094 B:2086-2094

Biological Unit 1 (1, 1)

	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	1	A:1086-1094 -

Biological Unit 2 (1, 1)

	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	1	- B:2086-2094

(no "Exon" information available for 4E3Y)

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:240
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:240
                                    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 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCK  265
               SCOP domains d4e3ya_ A: Sm endonuclease                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...................eeeeeeee........eeeeeee.......hhhhhh.hhhhhhhhhh.......hhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e3y A 1005 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCK 1244
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with NUCA_SERMA | P13717 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:240
                                    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 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCK  265
               SCOP domains d4e3yb_ B: Sm endonuclease                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....eeee......eeeeeeee...................hhhhh.hhhhhhhhhhhhheeeee..hhhhhh...hhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...................eeeeeeee........eeeeeee.......hhhhhh.hhhhhhhhhh.......hhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e3y B 2005 SIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCK 2244
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234      2244

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: 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	d4e3ya_	A:
1b	d4e3yb_	B:

(no "CATH Domain" information available for 4E3Y)

(no "Pfam Domain" information available for 4E3Y)

Asymmetric 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 Unit
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	Cis Peptide Bonds
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	NUCA_SERMA \| P13717	:	1g8t 1qae 1ql0 1smn

(no "Related Entries Specified in the PDB File" available for 4E3Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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