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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   STRUCTURAL REARRANGEMENT ACCOMPANYING NAD+ SYNTHESIS WITHIN A BACTERIAL DNA LIGASE CRYSTAL

Authors :   K. S. Gajiwala, C. Pinko

Date :   19 May 04 (Deposition) - 23 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (1x),B (1x)
Biol. Unit 6: C (1x),D (1x)

Keywords :   Nucleotidyl Transferase Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Gajiwala, C. Pinko
Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal.
Structure V. 12 1449 2004
PubMed-ID: 15296738 | Reference-DOI: 10.1016/J.STR.2004.05.017
(for further references see the PDB file header)

Molecule 1 - DNA LIGASE, NAD-DEPENDENT
	Chains	:	A, B, C, D
	EC Number	:	6.5.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ADENYLATION DOMAIN
	Gene	:	LIGA
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	226185
	Strain	:	V583

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A (1x)	B (1x)
Biological Unit 6 (1x)	:			C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 30)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	24	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 7)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 8)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 7)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:30 , LEU A:124 , ALA A:125 , ARG A:141 , ARG A:202 , HOH A:416 , HOH A:453	BINDING SITE FOR RESIDUE SO4 A 405
02	AC2	SOFTWARE	LYS A:79 , PRO A:81 , ARG A:129 , ARG A:137	BINDING SITE FOR RESIDUE SO4 A 406
03	AC3	SOFTWARE	ARG A:190 , PHE A:198 , ARG A:220	BINDING SITE FOR RESIDUE SO4 A 407
04	AC4	SOFTWARE	PRO A:81 , HIS A:82 , ASP A:83 , SER A:127 , ARG A:129 , ARG A:137 , GLU A:171 , ARG A:173 , HOH A:415	BINDING SITE FOR RESIDUE SO4 A 408
05	AC5	SOFTWARE	SER A:26 , TYR A:30 , TYR A:42 , ARG A:68 , LYS A:306 , NAD A:401 , HOH A:413 , HOH A:422	BINDING SITE FOR RESIDUE SO4 A 409
06	AC6	SOFTWARE	THR C:304 , ARG C:309 , HOH C:445	BINDING SITE FOR RESIDUE SO4 C 410
07	AC7	SOFTWARE	ARG A:14 , TRP B:268 , HIS B:275 , TYR B:314	BINDING SITE FOR RESIDUE SO4 A 411
08	AC8	SOFTWARE	TYR B:30 , LEU B:124 , ALA B:125 , ARG B:141 , ARG B:202 , HOH B:537 , HOH B:566 , HOH B:575 , HOH B:581	BINDING SITE FOR RESIDUE SO4 B 412
09	AC9	SOFTWARE	ARG B:129 , ARG B:137 , HOH B:561 , HOH B:577	BINDING SITE FOR RESIDUE SO4 B 413
10	BC1	SOFTWARE	HIS B:82 , ASP B:83 , SER B:127 , ARG B:129 , ARG B:137 , GLU B:171 , ARG B:173 , HOH B:555	BINDING SITE FOR RESIDUE SO4 B 415
11	BC2	SOFTWARE	HOH A:426 , TYR B:177 , PRO B:179 , ASN B:223 , ARG B:253	BINDING SITE FOR RESIDUE SO4 B 417
12	BC3	SOFTWARE	THR B:304 , ARG B:309	BINDING SITE FOR RESIDUE SO4 B 418
13	BC4	SOFTWARE	TRP A:268 , GLU A:272 , HIS A:275 , TYR A:314 , ARG B:14 , GLN B:21	BINDING SITE FOR RESIDUE SO4 B 419
14	BC5	SOFTWARE	VAL B:160 , PRO B:161 , MET B:162 , ARG B:163	BINDING SITE FOR RESIDUE SO4 B 420
15	BC6	SOFTWARE	TYR C:30 , LEU C:124 , ALA C:125 , ARG C:141 , ARG C:202 , HOH C:434 , HOH C:457	BINDING SITE FOR RESIDUE SO4 C 421
16	BC7	SOFTWARE	PRO C:81 , ARG C:129 , ARG C:137	BINDING SITE FOR RESIDUE SO4 C 422
17	BC8	SOFTWARE	HIS C:82 , ASP C:83 , SER C:127 , ARG C:129 , ARG C:137 , GLU C:171 , ARG C:173 , HOH C:430	BINDING SITE FOR RESIDUE SO4 C 423
18	BC9	SOFTWARE	TRP C:268 , GLU C:272 , HIS C:275 , TYR C:314	BINDING SITE FOR RESIDUE SO4 C 424
19	CC1	SOFTWARE	TYR D:30 , LEU D:124 , ALA D:125 , ARG D:141 , ARG D:202 , HOH D:537 , HOH D:570	BINDING SITE FOR RESIDUE SO4 D 425
20	CC2	SOFTWARE	ARG D:129 , ARG D:137	BINDING SITE FOR RESIDUE SO4 D 426
21	CC3	SOFTWARE	ARG D:190 , ARG D:220	BINDING SITE FOR RESIDUE SO4 D 427
22	CC4	SOFTWARE	PRO D:81 , HIS D:82 , ASP D:83 , SER D:127 , ARG D:129 , ARG D:137 , GLU D:171 , ARG D:173 , HOH D:556	BINDING SITE FOR RESIDUE SO4 D 428
23	CC5	SOFTWARE	THR D:304 , ARG D:309	BINDING SITE FOR RESIDUE SO4 D 429
24	CC6	SOFTWARE	HIS D:275 , TYR D:314 , HOH D:552	BINDING SITE FOR RESIDUE SO4 D 430
25	CC7	SOFTWARE	GLU B:38 , ASP B:39 , ASN B:200	BINDING SITE FOR RESIDUE NA B 531
26	CC8	SOFTWARE	TYR A:25 , TYR A:29 , TYR A:30 , VAL A:37 , GLU A:38 , ASP A:39 , TYR A:42 , ASP A:43 , SER A:88 , LEU A:89 , ASP A:91 , GLU A:118 , LEU A:119 , LYS A:120 , ILE A:121 , ALA A:125 , ARG A:141 , GLU A:175 , TYR A:227 , VAL A:289 , LYS A:291 , LYS A:315 , SO4 A:409 , HOH A:413 , HOH A:416	BINDING SITE FOR RESIDUE NAD A 401
27	CC9	SOFTWARE	TYR B:25 , SER B:26 , TYR B:29 , TYR B:30 , VAL B:37 , ASP B:39 , TYR B:42 , ASP B:43 , TYR B:87 , SER B:88 , LEU B:89 , ASP B:91 , GLU B:118 , LEU B:119 , LYS B:120 , ILE B:121 , ALA B:125 , ARG B:141 , GLU B:175 , TYR B:227 , VAL B:289 , LYS B:291 , LYS B:315 , HOH B:537 , HOH B:543	BINDING SITE FOR RESIDUE NAD B 402
28	DC1	SOFTWARE	SER C:26 , TYR C:29 , TYR C:30 , VAL C:37 , GLU C:38 , ASP C:39 , TYR C:42 , ASP C:43 , SER C:88 , LEU C:89 , ASP C:91 , GLU C:118 , LEU C:119 , LYS C:120 , ILE C:121 , ALA C:125 , ARG C:141 , GLU C:175 , TYR C:227 , VAL C:289 , LYS C:291 , LYS C:315 , HOH C:425 , HOH C:457	BINDING SITE FOR RESIDUE NAD C 403
29	DC2	SOFTWARE	TYR D:25 , TYR D:29 , TYR D:30 , VAL D:37 , ASP D:39 , TYR D:42 , ASP D:43 , TYR D:87 , SER D:88 , LEU D:89 , ASP D:91 , GLU D:118 , LEU D:119 , LYS D:120 , ILE D:121 , ALA D:125 , ARG D:141 , GLU D:175 , TYR D:227 , LYS D:291 , LYS D:315 , HOH D:534 , HOH D:537 , HOH D:545	BINDING SITE FOR RESIDUE NAD D 404

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	4	A:120-149 B:120-149 C:120-149 D:120-149

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	1	A:120-149 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	1	- B:120-149 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	1	- - C:120-149 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	1	- - - D:120-149

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	2	A:120-149 B:120-149 - -

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_LIGASE_N1	PS01055	NAD-dependent DNA ligase signature 1.	DNLJ_ENTFA	120-149	2	- - C:120-149 D:120-149

(no "Exon" information available for 1TAE)

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:321
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:321
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
           DNLJ_ENTFA     4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
               SCOP domains d1taea_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1taeA01 A:4-60 Helix hairpin bin                         ---------------------------1taeA02 A:88-123,A:254-324          1taeA03 A:124-253 DNA ligase/mRNA capping enzyme                                                                                  1taeA02 A:88-123,A:254-324  [code=3.30.1490.70, no name defined]        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..........eee.........ee.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: A:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tae A   4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain B from PDB  Type:PROTEIN  Length:321
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:321
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
           DNLJ_ENTFA     4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
               SCOP domains d1taeb_ B: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1taeB01 B:4-60 Helix hairpin bin                         ---------------------------1taeB02 B:88-123,B:254-324          1taeB03 B:124-253 DNA ligase/mRNA capping enzyme                                                                                  1taeB02 B:88-123,B:254-324  [code=3.30.1490.70, no name defined]        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..................eee.........ee.hhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhh....eeeeeeeee.......hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: B:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tae B   4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain C from PDB  Type:PROTEIN  Length:321
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:321
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
           DNLJ_ENTFA     4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
               SCOP domains d1taec_ C: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1taeC01 C:4-60 Helix hairpin bin                         ---------------------------1taeC02 C:88-123,C:254-324          1taeC03 C:124-253 DNA ligase/mRNA capping enzyme                                                                                  1taeC02 C:88-123,C:254-324  [code=3.30.1490.70, no name defined]        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..........eee........eee.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: C:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tae C   4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain D from PDB  Type:PROTEIN  Length:321
 aligned with DNLJ_ENTFA | Q837V6 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:321
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
           DNLJ_ENTFA     4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
               SCOP domains d1taed_ D: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1taeD01 D:4-60 Helix hairpin bin                         ---------------------------1taeD02 D:88-123,D:254-324          1taeD03 D:124-253 DNA ligase/mRNA capping enzyme                                                                                  1taeD02 D:88-123,D:254-324  [code=3.30.1490.70, no name defined]        CATH domains
           Pfam domains (1) -----DNA_ligase_aden-1taeD01 D:9-319                                                                                                                                                                                                                                                                                        -DNA_ Pfam domains (1)
           Pfam domains (2) -----DNA_ligase_aden-1taeD02 D:9-319                                                                                                                                                                                                                                                                                        -DNA_ Pfam domains (2)
           Pfam domains (3) -----DNA_ligase_aden-1taeD03 D:9-319                                                                                                                                                                                                                                                                                        -DNA_ Pfam domains (3)
           Pfam domains (4) -----DNA_ligase_aden-1taeD04 D:9-319                                                                                                                                                                                                                                                                                        -DNA_ Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........eeee........eee.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eeeehhhhhh..............eeeeeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhh.eeeeeeeee.......hhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------DNA_LIGASE_N1  PDB: D:120-149 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tae D   4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAETV 324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: ATP-grasp (191)

Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain (33)

Family: Adenylation domain of NAD+-dependent DNA ligase (16)

Protein domain: Adenylation domain of NAD+-dependent DNA ligase (14)

Enterococcus faecalis [TaxId: 1351] (9)

1a	d1taea_	A:
1b	d1taec_	C:
1c	d1taed_	D:
1d	d1taeb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: DNA ligase/mRNA capping enzyme (18)

Enterococcus faecalis v583. Organism_taxid: 226185. Strain: v583. (2)

1a	1taeA03	A:124-253
1b	1taeB03	B:124-253
1c	1taeC03	C:124-253
1d	1taeD03	D:124-253

Topology: Dna Ligase; domain 1 (375)

Homologous Superfamily: [code=3.30.1490.70, no name defined] (15)

Enterococcus faecalis v583. Organism_taxid: 226185. Strain: v583. (2)

2a	1taeA02	A:88-123,A:254-324
2b	1taeB02	B:88-123,B:254-324
2c	1taeC02	C:88-123,C:254-324
2d	1taeD02	D:88-123,D:254-324

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (10)

Enterococcus faecalis v583. Organism_taxid: 226185. Strain: v583. (2)

3a	1taeA01	A:4-60
3b	1taeB01	B:4-60
3c	1taeC01	C:4-60
3d	1taeD01	D:4-60

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DNLJ_ENTFA | Q837V6)

molecular function
	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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	1tae
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	DNLJ_ENTFA \| Q837V6	:	1ta8 3ba8 3ba9 3baa 3bab 4eeq 4efb 4efe 4lh6 4lh7

1ta8	NICOTINAMIDE MONONUCLEOTIDE (NMN) BOUND OPEN FORM OF THE SAME ENZYME

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (3, 30)

Sites (29, 29)

SS Bonds (0, 0)

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