3O0F - JenaLib

Title :   CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT PHOSPHOESTERASE (BAD_1165) FROM BIFIDOBACTERIUM ADOLESCENTIS ATCC 15703 AT 1.94 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   19 Jul 10 (Deposition) - 25 Aug 10 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : A

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. W. Han, J. Ko, C. L. Farr, M. C. Deller, Q. Xu, H. J. Chiu, M. D. Miller, J. Sefcikova, S. Somarowthu, P. J. Beuning, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson, M. J. Ondrechen
Crystal Structure Of A Metal-Dependent Phosphoesterase (Yp_910028. 1) From Bifidobacterium Adolescentis: Computational Prediction And Experimental Validation Of Phosphoesterase Activity.
Proteins V. 79 2146 2011
PubMed-ID: 21538547 | Reference-DOI: 10.1002/PROT.23035

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:24 , HIS A:85 , ARG A:109 , ARG A:112 , GLY A:144 , ARG A:145 , PRO A:146 , ARG A:161 , SER A:162 , PHE A:165 , GLY A:265 , LYS A:266 , PO4 A:305 , EDO A:307 , HOH A:362 , HOH A:467 , HOH A:474	BINDING SITE FOR RESIDUE AMP A 301
2	AC2	SOFTWARE	HIS A:19 , ASP A:24 , HIS A:49 , HIS A:262 , PO4 A:305	BINDING SITE FOR RESIDUE ZN A 302
3	AC3	SOFTWARE	GLU A:74 , HIS A:85 , HIS A:202 , FE A:304 , PO4 A:305 , HOH A:483	BINDING SITE FOR RESIDUE FE A 303
4	AC4	SOFTWARE	HIS A:17 , HIS A:19 , GLU A:74 , ASP A:260 , FE A:303 , PO4 A:305 , HOH A:483	BINDING SITE FOR RESIDUE FE A 304
5	AC5	SOFTWARE	HIS A:19 , ASP A:24 , HIS A:49 , GLU A:74 , HIS A:85 , ASP A:260 , HIS A:262 , LYS A:266 , AMP A:301 , ZN A:302 , FE A:303 , FE A:304 , HOH A:461 , HOH A:483	BINDING SITE FOR RESIDUE PO4 A 305
6	AC6	SOFTWARE	GLN A:35 , TRP A:261 , GLY A:269 , LEU A:270 , ARG A:281 , HOH A:398 , HOH A:437	BINDING SITE FOR RESIDUE EDO A 306
7	AC7	SOFTWARE	ASP A:24 , HIS A:49 , ARG A:109 , THR A:142 , GLY A:144 , PRO A:146 , AMP A:301	BINDING SITE FOR RESIDUE EDO A 307

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
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Chain A from PDB  Type:PROTEIN  Length:287
 aligned with A1A2L3_BIFAA | A1A2L3 from UniProtKB/TrEMBL  Length:300

    Alignment length:287
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
         A1A2L3_BIFAA     7 AEPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWDEATEASEEIGLPLLLGTEITAVDEDVSVHMLAFQYDPSNEHISSMFANTRAARLRRTKRMVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAGVYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDPQRNRRLLSDEQLDAMIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVTGGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------PHP-3o0fA01 A:14-244                                                                                                                                                                                                                   ------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhh..hhhhhhhhhhhh....hhhhhhh................hhhhhhhhhhhh..eeee.............hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeee....hhhhh.........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0f A   7 AEPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWDEATEASEEIGLPLLLGTEITAVDEDVSVHmLAFQYDPSNEHISSmFANTRAARLRRTKRmVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAGVYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDPQRNRRLLSDEQLDAmIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVTGGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR 293
                                    16        26        36        46        56        66        76        86        96    |  106       116       126       136       146       156       166       176       186       196       206       216    |  226       236       246       256       266       276       286       
                                                                                                          86-MSE        101-MSE        116-MSE                                                                                                  221-MSE

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 (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A1A2L3_BIFAA | A1A2L3)

molecular function
	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: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.

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