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Title :   CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

Authors :   J. Y. Lee, C. Chang, H. K. Song, S. T. Kwon, S. W. Suh

Date :   25 Nov 99 (Deposition) - 27 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Amp Complex, Nad+-Dependent, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Y. Lee, C. Chang, H. K. Song, J. Moon, J. K. Yang, H. K. Kim, S. T. Kwon, S. W. Suh
Crystal Structure Of Nad(+)-Dependent Dna Ligase: Modular Architecture And Functional Implications.
Embo J. V. 19 1119 2000
PubMed-ID: 10698952 | Reference-DOI: 10.1093/EMBOJ/19.5.1119
(for further references see the PDB file header)

Molecule 1 - DNA LIGASE
	Chains	:	A, B
	EC Number	:	6.5.1.2
	Organism Scientific	:	THERMUS FILIFORMIS
	Organism Taxid	:	276
	Other Details	:	AMP IS BONDED TO LYS116

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:406 , CYS A:409 , CYS A:422 , CYS A:427	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	CYS B:2406 , CYS B:2409 , CYS B:2422 , CYS B:2427	BINDING SITE FOR RESIDUE ZN B 2701
3	AC3	SOFTWARE	LEU A:85 , GLU A:114 , HIS A:115 , LYS A:116 , VAL A:117 , GLU A:169 , ARG A:196 , TYR A:221 , HIS A:253 , LYS A:312	BINDING SITE FOR RESIDUE AMP A 700
4	AC4	SOFTWARE	HOH B:1100 , LEU B:2085 , GLU B:2114 , HIS B:2115 , LYS B:2116 , VAL B:2117 , LEU B:2120 , GLU B:2169 , ARG B:2196 , TYR B:2221 , LYS B:2312	BINDING SITE FOR RESIDUE AMP B 2700

(no "SS Bond" information available for 1DGS)

(no "Cis Peptide Bond" information available for 1DGS)

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_THEFI	118-147	2	A:116-142 B:2116-2142
2	DNA_LIGASE_N2	PS01056	NAD-dependent DNA ligase signature 2.	DNLJ_THEFI	332-347	2	A:329-344 B:2329-2344

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_THEFI	118-147	1	A:116-142 -
2	DNA_LIGASE_N2	PS01056	NAD-dependent DNA ligase signature 2.	DNLJ_THEFI	332-347	1	A:329-344 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_THEFI	118-147	1	- B:2116-2142
2	DNA_LIGASE_N2	PS01056	NAD-dependent DNA ligase signature 2.	DNLJ_THEFI	332-347	1	- B:2329-2344

(no "Exon" information available for 1DGS)

Asymmetric 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:581
 aligned with DNLJ_THEFI | Q9ZHI0 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:586
                                                                                                                                                                                                                                                                    233                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                 232  |                                                                                                                                                                                                                                                                                                                                                               
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |  |  238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578      
          DNLJ_THEFI      1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYYEEGVLVFGATRGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGL--EESGLKSQYELLLWLKEKGFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEERPIRWPETCPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK  584
               SCOP domains d1dgsa3 A:1-314 Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                d1dgsa2 A:315-400 NAD+-dependent DNA ligase                                           d1dgsa1 A:401-581 NAD+-dependent DNA ligase, domain 3                                                                                                                                 SCOP domains
               CATH domains 1dgsA01 A:1-76 Helix hairpin bin                                            -------1dgsA02 A:84-118,A:251  -310         1dgs A03 A:119-25  0 DNA ligase/mRNA capping enzyme                                                                                    1dgsA02 A:84-118,A:251-310                                  ------1dgsA04 A:317-389 Nucleic acid-binding proteins                          ----------------------------------------1dgsA05 A:430-498 5' to 3' exonuclease, C-terminal subdomain         1dgsA06 A:499-581 5' to 3' exonuclease, C-terminal subdomain                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh...hhhhhh..........eee.........ee.hhhhhhhhhhhh....--....eeeeee....eee-eeee..eeeeee--....eee..hhhhh..............eeeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhh..eee................hhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhh.........eeeeee..hhhhhhh.........eeeee.....eeeeeeeeeeee.....eeeeeeeeeeee..eeeeeee..hhhhhhhh......eeeeeeehhheeeeeee.hhhh....................eee..eee.....hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:116-142 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N2   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dgs A    1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREA--EAPSLYTVEHKVDGLSV-LYYEEGVWSTGS--GDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK  581
                                    10        20        30        40        50        60        70        80        90       100    |  108       118   | | 127      |135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575      
                                                                                                                                  105  |             122 |        134  |                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                     106               123           135

Chain B from PDB  Type:PROTEIN  Length:581
 aligned with DNLJ_THEFI | Q9ZHI0 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:586
                                                                                                                                                                                                                                                                    233                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                 232  |                                                                                                                                                                                                                                                                                                                                                               
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |  |  238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578      
          DNLJ_THEFI      1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLERALGRKRPFLYTVEHKVDGLSVNLYYEEGVLVFGATRGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGL--EESGLKSQYELLLWLKEKGFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEERPIRWPETCPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELLEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK  584
               SCOP domains d1dgsb3 B:2001-2314 Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                            d1dgsb2 B:2315-2400 NAD+-dependent DNA ligase                                         d1dgsb1 B:2401-2581 NAD+-dependent DNA ligase, domain 3                                                                                                                               SCOP domains
               CATH domains 1dgsB01 B:2001-2076 Helix hairpin bin                                       -------1dgsB02 B:2084-2118,B:  2251-2310    1dgs B03 B:2119-2  250 DNA ligase/mRNA capping enzyme                                                                                  1dgsB02 B:2084-2118,B:2251-2310                             ------1dgsB04 B:2317-2389 Nucleic acid-binding proteins                        ----------------------------------------1dgsB05 B:2430-2498 5' to 3' exonuclease, C-terminal subdomain       1dgsB06 B:2499-2581 5' to 3' exonuclease, C-terminal subdomain                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........eee.........ee.hhhhhhhhhhhh....--....eeeeee....eee-eeee..eeeeee--....eee.hhhhhh..............eeeeeee...hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhh.....eeee............hhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhh.........eeeee.....eeeeeeeeeeee.....eeeeeeeeeee....eeeeee..hhhhhhhh......eeeeeeehhheeeeeee.hhhh....................eee..eee.....hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: B:2116-214------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N2   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dgs B 2001 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREA--EAPSLYTVEHKVDGLSV-LYYEEGVWSTGS--GDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK 2581
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100    | 2108      2118   | |2127      2135      2145      2155      2165      2175      2185      2195      2205      2215      2225      2235      2245      2255      2265      2275      2285      2295      2305      2315      2325      2335      2345      2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505      2515      2525      2535      2545      2555      2565      2575      
                                                                                                                                 2105  |            2122 |       2134  |                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                    2106              2123          2135

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

(no "Pfam Domain" information available for 1DGS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DNLJ_THEFI | Q9ZHI0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003911	DNA ligase (NAD+) activity	Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006266	DNA ligation	The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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