Structure of PDB 5tt5 Chain A

Receptor sequence
>5tt5A (length=581) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHP
ELITPDSPTQRVGAAPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQD
RLVTWCCELMLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAI
PLKLHGENIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAG
SLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQFKKWGLPVSD
RVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVAR
APRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSN
ATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFP
THCPVCGSDVERVEGEAVARCTGGLICGAQRKESLKHFVSRRAMDVDGMG
DKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKAKE
TTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIV
VASHVHNFFAEESNRNVISELLAEGVHWPAP
3D structure
PDB5tt5 Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases.
ChainA
Resolution1.552 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E113 M115 D117 Y225 K314 C408 C411 T427 C432
Catalytic site (residue number reindexed from 1) E108 M110 D112 Y220 K309 C403 C406 T422 C427
Enzyme Commision number 6.5.1.2: DNA ligase (NAD(+)).
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 NAD A H18 Y22 P28 I30 D32 Y35 D36 S81 L82 E113 M115 L116 A120 R136 E173 Y225 V288 K290 K314 H18 Y22 P28 I30 D32 Y35 D36 S81 L82 E108 M110 L111 A115 R131 E168 Y220 V283 K285 K309
BS02 ZN A C408 C411 C426 C432 C403 C406 C421 C427
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003911 DNA ligase (NAD+) activity
GO:0005515 protein binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
GO:0070403 NAD+ binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006266 DNA ligation
GO:0006281 DNA repair
GO:0006288 base-excision repair, DNA ligation
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5tt5, PDBe:5tt5, PDBj:5tt5
PDBsum5tt5
PubMed28223499
UniProtP15042|DNLJ_ECOLI DNA ligase (Gene Name=ligA)

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