Structure of PDB 6x9d Chain A

Receptor sequence

>6x9dA (length=1218) Species: 707241 (Sinorhizobium meliloti SM11)

APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPD
TATRDALIRDKIADGNWKSHLSRSLFVNAATWGLVVTGKLTSTVNDRSLA
AALTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKG
FSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIK
LSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLEL
SLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIM
VRLVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDV
VFPQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGK
LDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIA
DPVEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEA
LRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARR
AVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSA
LNAIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTG
QIAAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRV
GAALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQN
AMIVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLK
GALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLA
SETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNA
TGYGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGL
SGTGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAE
AEAARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQ
LAAALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGAL
VEGDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVS
ASINTAAAGGNASLMAIG

3D structure

• PDB: 6x9d Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
• Chain: A
• Resolution: 1.54 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N707 K730 E810 C844 E940 A1022
• Catalytic site (residue number reindexed from 1): N692 K715 E795 C829 E925 A1007
• 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 Y373 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 Q447 C448 E492 S498 F499	D291 A292 V323 Q325 R352 V354 K355 G356 A357 Y358 W359 F377 T378 R379 K380 T383 A406 T407 H408 N409 Q432 C433 E477 S483 F484
BS02	HYP	A	E674 F708 I712 R843 S845 G1002 A1003 F1010	E659 F693 I697 R828 S830 G987 A988 F995	MOAD: Ki=7mM
BS03	NAD	A	I703 S704 P705 W706 N707 I712 K730 A732 E733 G763 G766 A767 T781 G782 S783 V786 E810 T811 C844 E940 F942 F1010	I688 S689 P690 W691 N692 I697 K715 A717 E718 G748 G751 A752 T766 G767 S768 V771 E795 T796 C829 E925 F927 F995

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:6x9d, PDBe:6x9d, PDBj:6x9d
• PDBsum: 6x9d
• PubMed: 33333077
• UniProt: F7X6I3