1ZM8 - JenaLib

Title :   APO CRYSTAL STRUCTURE OF NUCLEASE A FROM ANABAENA SP.

Authors :   M. Ghosh, G. Meiss, A. Pingoud, R. E. London, L. C. Pedersen

Date :   10 May 05 (Deposition) - 21 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Nuca, Nuclease, Metal Dependent, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ghosh, G. Meiss, A. Pingoud, R. E. London, L. C. Pedersen
Structural Insights Into The Mechanism Of Nuclease A, A Beta Beta Alpha Metal Nuclease From Anabaena.
J. Biol. Chem. V. 280 27990 2005
PubMed-ID: 15897201 | Reference-DOI: 10.1074/JBC.M501798200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:155 , SO4 A:278 , HOH A:281 , HOH A:282 , HOH A:283 , HOH A:284	BINDING SITE FOR RESIDUE MN A 275
2	AC2	SOFTWARE	GLU A:136 , ASP A:246 , GLU A:249 , GLU A:269 , HOH A:285	BINDING SITE FOR RESIDUE MN A 276
3	AC3	SOFTWARE	GLU A:136 , GLU A:249 , ASP A:255 , PHE A:256 , GLN A:265 , GLU A:269	BINDING SITE FOR RESIDUE MN A 277
4	AC4	SOFTWARE	ARG A:93 , HIS A:124 , ASN A:155 , MN A:275 , HOH A:281 , HOH A:282 , HOH A:300 , HOH A:392	BINDING SITE FOR RESIDUE SO4 A 278
5	AC5	SOFTWARE	ARG A:109 , TYR A:165 , ARG A:222 , ARG A:239 , HOH A:323 , HOH A:408	BINDING SITE FOR RESIDUE SO4 A 279
6	AC6	SOFTWARE	ASP A:153 , LEU A:234 , ASN A:236	BINDING SITE FOR RESIDUE NA A 280

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:239
 aligned with NUCA_NOSS1 | P38446 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:239
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265         
           NUCA_NOSS1    36 ISVHLLLGNPSGATPTKLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVTPSMYSGSGYDRGHIAPSADRTKTTEDNAATFLMTNMMPQTPDNNRNTWGNLEDYCRELVSQGKELYIVAGPNGSLGKPLKGKVTVPKSTWKIVVVLDSPGSGLEGITANTRVIAVNIPNDPELNNDWRAYKVSVDELESLTGYDFLSNVSPNIQTSIESKVDN 274
               SCOP domains d1zm8a_ A: Nuclease NucA                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------Endonuclease_NS-1zm8A01 A:61-263                                                                                                                                                                           ----------- Pfam domains
         Sec.struct. author .hhhhh................eeee....eeeee....eeeeeeeeehhhhh......................hhhhh.....eeee..hhhhh..hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhh.....eeeeeeee.....hhhhhh.....eeeeeee.......hhhhhh.hhhhhhhhhh.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zm8 A  36 ISVHLLLGNPSGATPTKLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVTPSMYSGSGYARGHIAPSADRTKTTEDNAATFLMTNMMPQTPDNNRNTWGNLEDYCRELVSQGKELYIVAGPNGSLGKPLKGKVTVPKSTWKIVVVLDSPGSGLEGITANTRVIAVNIPNDPELNNDWRAYKVSVDELESLTGYDFLSNVSPNIQTSIESKVDN 274
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NUCA_NOSS1 | P38446)

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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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