4B08 - JenaLib

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:827
 aligned with DPOA_YEAST | P13382 from UniProtKB/Swiss-Prot  Length:1468

    Alignment length:880
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228
          DPOA_YEAST    349 TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLER 1228
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeeeee.....eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeee..........eeeeeeeeee...................eeeee....hhhhhhhhhh......eeee...............eeeee.hhh.eee........eeeeeeeeeeeee....eeeeeeeeeeeeeee.............eeeeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh...........----..hhhhhhhhhh...eeee..hhhhhhh.......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......--------------------------------......eee...eeeee..hhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeee.-------.eeeeee.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh.....hhhhhhhhhhhhhh.......eeeeee...----------.......eeehhhhhhhhhh...hhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4b08 A  349 TDTFQmFWLDYCEVNNTLILFGKVKLKDDNCVSAmVQINGLCRELFFLPREGKTPTDIHEEIIPLLmDKYGLDNIRAKPQKmKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRImGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTmPNLRCLSLSIQTLmNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAmLSCFCAmLKVEDPDVIIGHRLQNVYLDVLAHRmHDLNIPTFSSIGRRLRRTWPEKF----SNmNHFFISDICSGRLICDIANEmGQSLTPKCQSWDLSEmYQVTCEKEHKPLDIDYQNPQYQNDVNSmTmALQENITNCmISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDK--------------------------------VFEPEKGLHKNYVLVmDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVmKTETDPHKRVQCDIRQQALKLTANSmYGCLGYVNSRFYAKPLAmLVTNKGREILmNTRQLAESmNLLVVYGDTDSVmIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVN-------TTVLEVKGLDmKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINmKLSKDPKAYPGGKNmPAVQVALRmRKAGRVVKAGSVITFVITKQ----------ALSVAERAHALNEVmIKSNNLIPDPQYYLEKQIFAPVERLLER 1228
                                 | 358       368       378    |  388       398       408      |418       428 |     438       448       458       468       478       488   |   498       508       518       528    |  538       548       558       568       578       588       598       608       618|      628       638       648   |   658       668      |  - | |   688       698    |  708       718|      728       738       748|      758|      768       778       788       798       808      |  -         -         -       848       858    |  868       878       888       898       908       918     | 928       938       948 |     958       968       978|      988       998  |   1008      1018      1028      1038      1048      |  -    | 1068    | 1078      1088      1098      1108      1118      1128  |   1138      1148      1158      1168      |  -      1188      1198 |    1208      1218      1228
                                 |                          383-MSE                         415-MSE        430-MSE                                                       492-MSE                                  533-MSE       547-MSE                                                                 619-MSE  |                       652-MSE                675  680 |                  703-MSE         719-MSE                     747-MSE     759-MSE                                                 815                              848            863-MSE                                                      924-MSE                   950-MSE           968-MSE    979-MSE  988-MSE     1001-MSE                                              1055    1063      1073-MSE                                                  1131-MSE       1146-MSE 1155-MSE            1175       1186          1200-MSE                        
                               354-MSE                                                                                                                                                                                                                                                                         626-MSE                                                 682-MSE                                                            749-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 '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPOA_YEAST | P13382)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0001882	nucleoside binding	Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
	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.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	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:0006270	DNA replication initiation	The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
	GO:0000731	DNA synthesis involved in DNA repair	Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
	GO:0006278	RNA-dependent DNA biosynthetic process	A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0006273	lagging strand elongation	The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
	GO:0006272	leading strand elongation	The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006279	premeiotic DNA replication	The replication of DNA that precedes meiotic cell division.
cellular component
	GO:0005658	alpha DNA polymerase:primase complex	A complex of four polypeptides, comprising large and small DNA polymerase alpha subunits and two primase subunits, which catalyzes the synthesis of an RNA primer on the lagging strand of replicating DNA; the smaller of the two primase subunits alone can catalyze oligoribonucleotide synthesis.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 28)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (25, 25)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File