Structure of PDB 6vz9 Chain A

Receptor sequence

>6vz9A (length=1217) Species: 707241 (Sinorhizobium meliloti SM11)

APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPD
TATRDALIRDKIADGNWKSHSRSLFVNAATWGLVVTGKLTSTVNDRSLAA
ALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGF
SYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKL
SALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELS
LDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMV
RLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVV
FPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKL
DRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIAD
PVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEAL
RESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRA
VRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSAL
NAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQ
IAAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVG
AALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNA
MIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKG
ALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLAS
ETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNAT
GYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLS
GTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEA
EAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQL
AAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALV
EGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSA
SINTAAAGGNASLMAIG

3D structure

• PDB: 6vz9 Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate.
• Chain: A
• Resolution: 1.52 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N707 K730 E810 C844 E940 A1022
• Catalytic site (residue number reindexed from 1): N691 K714 E794 C828 E924 A1006
• Enzyme Commision number: 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
  1.5.5.2: proline dehydrogenase.

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	FAD	A	D306 A307 V338 Q340 R367 V369 K370 G371 A372 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 Q447 C448 L449 E492 S498 F499	D290 A291 V322 Q324 R351 V353 K354 G355 A356 W358 F376 T377 R378 K379 T382 A405 T406 H407 N408 Q431 C432 L433 E476 S482 F483
BS02	NAD	A	I703 S704 P705 W706 N707 I712 K730 A732 E733 G763 G766 F780 T781 G782 S783 V786 I790 E810 T811 C844 E940 F942 F1010	I687 S688 P689 W690 N691 I696 K714 A716 E717 G747 G750 F764 T765 G766 S767 V770 I774 E794 T795 C828 E924 F926 F994
BS03	T2C	A	K265 D306 Y473 Y485 R488 R489	K249 D290 Y457 Y469 R472 R473

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity
• GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
• GO:0004657 proline dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0006560 proline metabolic process
• GO:0006561 proline biosynthetic process
• GO:0006562 proline catabolic process
• GO:0010133 proline catabolic process to glutamate

Cellular Component

• GO:0009898 cytoplasmic side of plasma membrane

External links

• PDB: RCSB:6vz9, PDBe:6vz9, PDBj:6vz9
• PDBsum: 6vz9
• PubMed: 32159324
• UniProt: F7X6I3