Structure of PDB 6x9b Chain A

Receptor sequence

>6x9bA (length=1214) Species: 707241 (Sinorhizobium meliloti SM11)

APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTAT
RDALIRDKIADGNWKSHLRSLFVNAATWGLVVTGKLTSTVNDRSLAAALT
RLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYS
YDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSAL
HPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDL
LEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLV
KGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQ
FATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRP
CRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVE
VVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRES
AAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRL
AADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAI
AEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAA
ALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAAL
VAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIV
DSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALH
ELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETG
VGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYG
LTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTG
PKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAA
RNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLAAA
LATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGD
AERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASIN
TAAAGGNASLMAIG

3D structure

• PDB: 6x9b Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
• Chain: A
• Resolution: 1.46 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N707 K730 E810 C844 E940 A1022
• Catalytic site (residue number reindexed from 1): N688 K711 E791 C825 E921 A1003
• 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 R367 V369 K370 G371 A372 Y373 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 Q447 C448 Y473 E492 S498 F499	D287 A288 V319 R348 V350 K351 G352 A353 Y354 W355 F373 T374 R375 K376 T379 A402 T403 H404 N405 Q428 C429 Y454 E473 S479 F480
BS02	NAD	A	I703 S704 P705 W706 N707 I712 K730 A732 E733 G763 G766 A767 T781 G782 S783 V786 I790 E810 T811 C844 E940 F942	I684 S685 P686 W687 N688 I693 K711 A713 E714 G744 G747 A748 T762 G763 S764 V767 I771 E791 T792 C825 E921 F923
BS03	UYA	A	E674 F708 S845 G1002 A1003 F1010	E655 F689 S826 G983 A984 F991	MOAD: Ki=8mM

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:6x9b, PDBe:6x9b, PDBj:6x9b
• PDBsum: 6x9b
• PubMed: 33333077
• UniProt: F7X6I3