2YB1 - JenaLib

Title :   STRUCTURE OF AN AMIDOHYDROLASE FROM CHROMOBACTERIUM VIOLACEUM (EFI TARGET EFI-500202) WITH BOUND MN, AMP AND PHOSPHATE.

Authors :   M. W. Vetting, B. Hillerich, R. Foti, R. D. Seidel, W. D. Zencheck, R. Tor H. J. Imker, F. M. Raushel, J. A. Gerlt, S. C. Almo

Date :   25 Feb 11 (Deposition) - 16 Mar 11 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Cummings, M. W. Vetting, S. V. Ghodge, C. Xu, B. Hillerich, R. D. Seidel, S. C. Almo, F. M. Raushel
Prospecting For Unannotated Enzymes: Discovery Of A 3', 5'-Nucleotide Bisphosphate Phosphatase Within The Amidohydrolase Superfamily.
Biochemistry V. 53 591 2014
PubMed-ID: 24401123 | Reference-DOI: 10.1021/BI401640R

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:14 , HIS A:39 , HIS A:250 , AMP A:1292 , PO4 A:1293	BINDING SITE FOR RESIDUE MN A 1289
2	AC2	SOFTWARE	HIS A:7 , HIS A:9 , GLU A:64 , ASP A:248 , MN A:1291 , PO4 A:1293	BINDING SITE FOR RESIDUE MN A 1290
3	AC3	SOFTWARE	GLU A:64 , HIS A:75 , HIS A:191 , MN A:1290 , PO4 A:1293	BINDING SITE FOR RESIDUE MN A 1291
4	AC4	SOFTWARE	ASP A:14 , HIS A:39 , ARG A:99 , ARG A:102 , SER A:133 , ARG A:134 , THR A:135 , PHE A:154 , HIS A:250 , MN A:1289 , PO4 A:1293 , HOH A:2268 , HOH A:2269 , HOH A:2270	BINDING SITE FOR RESIDUE AMP A 1292
5	AC5	SOFTWARE	HIS A:7 , HIS A:9 , HIS A:39 , GLU A:64 , HIS A:75 , HIS A:191 , ARG A:194 , ASP A:248 , HIS A:250 , MN A:1289 , MN A:1290 , MN A:1291 , AMP A:1292 , HOH A:2271	BINDING SITE FOR RESIDUE PO4 A 1293

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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
	(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:284
 aligned with 35NBP_CHRVO | Q7NXD4 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:287
                                                                                                                                                                                                                                                                                                                     285   
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   |   
          35NBP_CHRVO     2 ANIDLHFHSRTSDGALTPTEVIDRAAARAPALLALTDHDCTGGLAEAAAAAARRGIPFLNGVEVSVSWGRHTVHIVGLGIDPAEPALAAGLKSIREGRLERARQMGASLEAAGIAGCFDGAMRWCDNPEMISRTHFARHLVDSGAVKDMRTVFRKYLTPGKPGYVSHQWASLEDAVGWIVGAGGMAVIAHPGRYDMGRTLIERLILDFQAAGGQGIEVASGSHSLDDMHKFALHADRHGLYASSGSDFHAPGEGGRDVGHTEDLPPICRPIWRELEARILRPAD---   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee............hhhhhhhhhhh....eeee.......hhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhh..............hhhhhhhhhhhh..eeee.hhhhh..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.eeeee........---.............hhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yb1 A   2 ANIDLHFHSRTSDGALTPTEVIDRAAARAPALLALTDHDCTGGLAEAAAAAARRGIPFLNGVEVSVSWGRHTVHIVGLGIDPAEPALAAGLKSIREGRLERARQMGASLEAAGIAGCFDGAMRWCDNPEMISRTHFARHLVDSGAVKDMRTVFRKYLTPGKPGYVSHQWASLEDAVGWIVGAGGMAVIAHPGRYDMGRTLIERLILDFQAAGGQGIEVASGSHSLDDMHKFALHADRHGLYASSGSDFHAPGE---DVGHTEDLPPICRPIWRELEARILRPADAEN 288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  |   |261       271       281       
                                                                                                                                                                                                                                                                                      254 258

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (35NBP_CHRVO | Q7NXD4)

molecular function
	GO:0097657	3',5'-nucleotide bisphosphate phosphatase activity	Catalysis of the reaction: 3',5'-nucleotide bisphosphate + H20 = 5'-nucleotide monophosphate + phosphate.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

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