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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER

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

Date :   03 Mar 99 (Deposition) - 18 May 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

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

Reference :   M. D. Miller, J. Cai, K. L. Krause
The Active Site Of Serratia Endonuclease Contains A Conserved Magnesium-Water Cluster.
J. Mol. Biol. V. 288 975 1999
PubMed-ID: 10329193 | Reference-DOI: 10.1006/JMBI.1999.2729
(for further references see the PDB file header)

Molecule 1 - PROTEIN (EXTRACELLULAR ENDONUCLEASE)
	Cellular Location	:	EXTRACELLULAR
	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 Strain	:	PROTEASE DEFICIENT STRAIN
	Expression System Taxid	:	615
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Strain	:	SM6

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:119 , HOH A:252 , HOH A:253 , HOH A:254 , HOH A:255 , HOH A:256	BINDING SITE FOR RESIDUE MG A 251
2	AC2	SOFTWARE	ASN B:119 , HOH B:252 , HOH B:253 , HOH B:254 , HOH B:255 , HOH B:256	BINDING SITE FOR RESIDUE MG B 251
3	ASA	AUTHOR	HIS A:89 , GLU A:127 , ASN A:119 , MG A:251 , HOH A:252 , HOH A:253 , HOH A:254 , HOH A:255 , HOH A:256	ACTIVE SITE REGION IN MONOMER A WITH CATALYTIC MAGNESIUM WATER CLUSTER
4	ASB	AUTHOR	HIS B:89 , GLU B:127 , ASN B:119 , MG B:251 , HOH B:252 , HOH B:253 , HOH B:254 , HOH B:255 , HOH B:256	ACTIVE SITE REGION IN MONOMER B WITH CATALYTIC MAGNESIUM WATER CLUSTER

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 1QAE)

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

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 1QAE)

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

    Alignment length:240
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
           NUCA_SERMA    27 IDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1qaea_ A: Sm endonuclease                                                                                                                                                                                                                       SCOP domains
               CATH domains 1qaeA00 A:6-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................ee....eeee......eeeeeeee....................hhh...hhhh..hhhhh.eeeee...hhhh.....hhhhh.hhheeeeehhhh..hhhhhhhhhhhh........eeeeeeee...................eeeeeeee........eeeeeee........hhhh...hhhhhhhh.........hhhhhhh......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qae A   6 IDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

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

    Alignment length:240
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
           NUCA_SERMA    27 IDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 266
               SCOP domains d1qaeb_ B: Sm endonuclease                                                                                                                                                                                                                       SCOP domains
               CATH domains 1qaeB00 B:6-245 Extracellular Endonuclease, subunit A                                                                                                                                                                                            CATH domains
           Pfam domains (1) ------------------Endonuclease_NS-1qaeB01 B:24-225                                                                                                                                                                          -------------------- Pfam domains (1)
           Pfam domains (2) ------------------Endonuclease_NS-1qaeB02 B:24-225                                                                                                                                                                          -------------------- Pfam domains (2)
         Sec.struct. author .................ee....eeee......eeeeeeee....................hhh...hhhh..hhhhh.eeeee...hhhh.....hhhhh.hhheeeeehhhh..hhhhhhhhhhhh........eeeeeeee...................eeeeeeee........eeeeeee........hhhh...hhhhhhhh.........hhhhhhh......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qae B   6 IDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN 245
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

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	d1qaea_	A:
1b	d1qaeb_	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	1qaeA00	A:6-245
1b	1qaeB00	B:6-245

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: His-Me_finger (38)

Family: Endonuclease_NS (14)

Serratia marcescens (3)

1a	Endonuclease_NS-1qaeB01	B:24-225
1b	Endonuclease_NS-1qaeB02	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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	1qae
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	3.1.30.2
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	NUCA_SERMA \| P13717	:	1g8t 1ql0 1smn 4e3y

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

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

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