Structure of PDB 7r77 Chain A

Receptor sequence

>7r77A (length=1830) Species: 235443 (Cryptococcus neoformans var. grubii H99)

DIKAAVRNMSDDLPPISDIEAMFDHLVSRIPDIVELVRQLNGRKLRVATM
CSGTESPLLALNMIAKAIKAQHGLTLAFEHVFSCEIEPFKQAYIERNFTP
PILFRDVTELGKKRAHTAYGSMVDVPGDVDILIAGTSCVDYSSGRTFRGM
LQWVKKHQPPIVILENVCNAPWDKVVEYFGQIDYDAQYTRLDTKEFYIPH
TRTRVYLFATPSDLPEKWAQTVKDLRRPWSSPFEAFLLHTDDPNIHRARL
ELASARAQTSRKTTDWNRCESRHQRARQDEALGLLRPLTSWQEAGVCKGL
DWTWNDWLLAQTERVVDLLEISTLRMAKDGIDSGFKACIWNVSQNVDRQT
GSSKTALAPCLTPNMIPWVTIRGGPVTGREALALQGIPVRELLLTSENED
QLADLAGNAMTTTVVGSAMIAALKVACHKITEGANPEKEAALILEKEAVD
DEQVANRIIGEDYLEHHDLDLAKVTKSNLSEILDLACRSSRHCQCEGQSG
TAPNILECQECSYRACKSCGGRPEHVYAPCANQRVEPAEFEKRFKGLLPM
RVRIAGLTDQCLNAVRKAAEKSNKGSVNDNDWQLWSTALLEGIHDAEFRF
RYLKRQSTWTAVYEARRAMLSLVLRNQIPEWRLTIKAPASEPNNSQLRAL
LLHPVARLQIDIAGQDVLCGPWELCIPSMKTIDIEITGKGELLPSWQASL
GLQGPFANTTRWSEVEISLQAEDENTLDRKLSGTYQLLPRCGQAMSSLHK
KRPDLSDDGLPQLYFFLDPTRCGESREDRYVFSTSTERLDYGTERPVIAR
LDSHWREGNEKQRKVKLDVSGAWVKCPEAHLTAIRATFAIPSSASAISAS
LTTEGCSHAMALLSCRVPLDPTHSESMWRRGAWAEIDLSHQGNTTFANLA
WITERLPPLDGLKNWAHIADDVSEHVCERCAPRPPKIHWIKTIIAFEDKL
EAGQYEHALKHRPSPFVVQLRLDQDIGSFRIGLNIVSLAHRALSRLPPTT
SEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPENSQFKLPLRKEQLR
SLWWMLEQEKATGKTHTFVEEEISESLLPAVGWRAEGKAERPVMVRGGVI
ADQVGYGKTVISIALVAQTLSLPAPEPATPGLIDLKATLIVVPGHLSKQW
PNEIARFTGSMFKVIVIQGMKDLQEKTIAELGKADIIVMASEIFESDVYW
SRLEYLSAQPREWLHDTQGGRFFCDRLDAAMESLVSQTKILKLLPNPVLH
MFRFRRVIADEFTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIA
TFMGIHLGVEDDGEGDVQYQKARAKDQTQAEKFHAFREVHSRAWHNRRDE
LAQEFLNVFVRQNIAEIEDIPTVEHIHTFKLPASEGAVYLELEHHLQALE
MQARKETKFKNVSQGDRNARLEEALSDSKTAEEALLKRCCHFTLDLSDKT
QDAKSAQEACDHITSARARQLLACQEDLSRSVNQAIALHGWIKKKGGFRQ
PFAEWIAFSSNISKHQGDIEAARILLKVIEKCGVKDGNIPPSPSDKQSPS
KMDDVKWQLREQTHLLRKLVKELVARVRSLRFFEVVRKIQKGKSDAQIVL
ESSECGHKPSTNPDIEMAILSCCGHVACHKCMRKAAASQRCVKSGECQAA
VRPTNIVKVSSLGVEGELSSGRYGAKLEHLVNLIHSIPKNERVLVFLQWE
DLAGKVSEALSAGRIPHVTLSGSAKSRANTLDRFQADSARVLLLKMNDSN
LTTANHAVFLGPLFTNSLFNYRAVETQAIGRVRRYGQQKKVHIHRLLALD
TIDMTIFNARRTELKEKTDWEEIPQEEYKG

3D structure

• PDB: 7r77 Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

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	dna	A	R592 C593 R596 T636 R638 Q668 N669 R672 R2036	R268 C269 R272 T312 R314 Q344 N345 R348 R1560
BS02	dna	A	C484 N485 R518 T519 Q668 T686	C168 N169 R202 T203 Q344 T362
BS03	ZN	A	C817 C819 C843	C493 C495 C519
BS04	ZN	A	C1200 C1271 C1274 H1348	C856 C927 C930 H990
BS05	ZN	A	C832 C835 H849 C1065	C508 C511 H525 C741
BS06	ZN	A	C2081 H2083 C2104 C2107	C1605 H1607 C1628 C1631
BS07	ZN	A	C2099 H2101 C2123	C1623 H1625 C1647

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003886 DNA (cytosine-5-)-methyltransferase activity
• GO:0005524 ATP binding
• GO:0008094 ATP-dependent activity, acting on DNA
• GO:0008168 methyltransferase activity
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0043565 sequence-specific DNA binding
• GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity
• GO:0140658 ATP-dependent chromatin remodeler activity

Biological Process

• GO:0006289 nucleotide-excision repair
• GO:0006338 chromatin remodeling
• GO:0006346 DNA methylation-dependent heterochromatin formation
• GO:0009889 regulation of biosynthetic process
• GO:0032259 methylation

Cellular Component

• GO:0005634 nucleus
• GO:0005694 chromosome

External links

• PDB: RCSB:7r77, PDBe:7r77, PDBj:7r77
• PDBsum: 7r77
• PubMed: 35202575
• UniProt: J9VI03|DMT5_CRYNH DNA (cytosine-5-)-methyltransferase DMT5 (Gene Name=DMT5)