Structure of PDB 6x9c Chain B

Receptor sequence

>6x9cB (length=1208) Species: 707241 (Sinorhizobium meliloti SM11)

PAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAA
ASTARKLIEALRGKSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATR
DALIRDKIADGNWKSHLRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTR
LISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFSYSY
DMLEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLSALHP
RYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLE
VLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKG
AYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFA
THNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCR
IYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADPVEVV
RAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALRESAA
MKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAVRLAA
DAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAIAE
VREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAAL
VAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAALVA
AAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAMIVDS
SALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGALHEL
HIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASETGVG
TFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGYGLT
FGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPK
AGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAEAARN
AGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLAAALA
TGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVEGDAE
RIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSASINTA
AAGGNASL

3D structure

• PDB: 6x9c Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
• Chain: B
• Resolution: 1.44 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N707 K730 E810 C844 E940 A1022
• Catalytic site (residue number reindexed from 1): N686 K709 E789 C823 E919 A1001
• 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	NAI	B	I703 S704 P705 W706 N707 K730 E733 G763 G766 A767 F780 G782 S783 V786 I790 C844 E940 F942	I682 S683 P684 W685 N686 K709 E712 G742 G745 A746 F759 G761 S762 V765 I769 C823 E919 F921
BS02	FDA	B	D306 A307 V338 Q340 R367 V369 K370 G371 A372 Y373 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 Q447 C448 Y473 E492 S498 F499	D285 A286 V317 Q319 R346 V348 K349 G350 A351 Y352 W353 F371 T372 R373 K374 T377 A400 T401 H402 N403 Q426 C427 Y452 E471 S477 F478
BS03	PRO	B	E674 F708 C844 S845 G1002 A1003 F1010	E653 F687 C823 S824 G981 A982 F989	MOAD: Ki=11mM

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:6x9c, PDBe:6x9c, PDBj:6x9c
• PDBsum: 6x9c
• PubMed: 33333077
• UniProt: F7X6I3