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(-) Description

Title :  1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.
 
Authors :  E. Inagaki, K. Sakamoto, M. Nishio, S. Yokoyama
Date :  19 Sep 06  (Deposition) - 16 Oct 07  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Glutamate, Type Ii Hyperprolinmia, Oxidoreductase, 1-Pyrroline-5-Carboxylate, Proline Methabolic Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Inagaki, K. Sakamoto, M. Nishio, S. Yokoyama, T. H. Tahirov
Crystal Structure Of Ternary Complex Of Delta1- Pyrroline-5-Carboxylate Dehydrogenase With Substrate Mimic And Co-Factoer
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
    ChainsA, B
    EC Number1.5.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GLY2Mod. Amino AcidGLYCINE
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5NA2Ligand/IonSODIUM ION
6NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (5, 51)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2GLY6Mod. Amino AcidGLYCINE
3MPD18Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD9Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5NA-1Ligand/IonSODIUM ION
6NAD6Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:323 , GLY A:477 , ALA A:478 , PHE A:485 , HOH A:2246 , HOH A:2529 , HOH A:2541 , HOH A:2572BINDING SITE FOR RESIDUE GLY A1517
02AC2SOFTWAREILE A:180 , ALA A:181 , PRO A:182 , TRP A:183 , ASN A:184 , ILE A:189 , LYS A:207 , ALA A:209 , GLU A:210 , GLY A:240 , GLU A:241 , GLY A:244 , ALA A:245 , PHE A:258 , THR A:259 , GLY A:260 , SER A:261 , VAL A:264 , GLU A:288 , THR A:289 , GLY A:290 , CYS A:322 , GLU A:417 , PHE A:419 , PHE A:485 , ACT A:1519 , HOH A:2323 , HOH A:2324 , HOH A:2573 , HOH A:2574 , HOH A:2575 , HOH A:2576 , HOH A:2577 , HOH A:2578 , HOH A:2579BINDING SITE FOR RESIDUE NAD A1518
03AC3SOFTWAREALA A:245 , GLU A:249 , ALA A:271 , NAD A:1518 , HOH A:2580BINDING SITE FOR RESIDUE ACT A1519
04AC4SOFTWAREARG A:462 , PHE A:464 , HIS A:465 , HOH A:2581 , HOH A:2582 , LYS B:510BINDING SITE FOR RESIDUE ACT A1520
05AC5SOFTWARELEU A:275 , GLN A:279 , HOH A:2583 , HOH A:2584 , HOH A:2585BINDING SITE FOR RESIDUE MRD A1521
06AC6SOFTWAREPHE A:6 , TYR A:144 , ALA A:148 , HOH A:2262 , HOH A:2586 , HOH A:2587 , HOH A:2588 , GLU B:158BINDING SITE FOR RESIDUE MPD A1522
07AC7SOFTWAREARG A:151 , TYR A:171 , HOH A:2269 , HOH A:2555 , HOH A:2589BINDING SITE FOR RESIDUE MPD A1523
08AC8SOFTWAREARG A:36 , PRO A:39 , HOH A:2309BINDING SITE FOR RESIDUE MPD A1524
09AC9SOFTWARESER A:55 , LEU A:56 , GLU A:123 , ASP A:211 , HOH A:2143 , HOH A:2426BINDING SITE FOR RESIDUE NA A1525
10BC1SOFTWARESER B:323 , GLY B:477 , ALA B:478 , PHE B:485 , HOH B:2236 , HOH B:2377 , HOH B:2515 , HOH B:2556BINDING SITE FOR RESIDUE GLY B1517
11BC2SOFTWAREILE B:180 , ALA B:181 , PRO B:182 , TRP B:183 , ASN B:184 , ILE B:189 , LYS B:207 , ALA B:209 , GLU B:210 , GLY B:240 , GLY B:244 , ALA B:245 , PHE B:258 , THR B:259 , GLY B:260 , SER B:261 , VAL B:264 , GLU B:288 , THR B:289 , GLY B:290 , CYS B:322 , GLU B:417 , PHE B:419 , LEU B:445 , PHE B:485 , ACT B:1519 , HOH B:2557 , HOH B:2558 , HOH B:2559 , HOH B:2560 , HOH B:2561 , HOH B:2562 , HOH B:2563BINDING SITE FOR RESIDUE NAD B1518
12BC3SOFTWAREALA B:245 , GLU B:249 , ILE B:268 , ALA B:271 , NAD B:1518 , HOH B:2564BINDING SITE FOR RESIDUE ACT B1519
13BC4SOFTWARELYS A:510 , ARG B:462 , PHE B:464 , HIS B:465 , HOH B:2565 , HOH B:2566BINDING SITE FOR RESIDUE ACT B1520
14BC5SOFTWAREARG B:151 , HOH B:2540BINDING SITE FOR RESIDUE MPD B1521
15BC6SOFTWAREGLU A:158 , VAL A:160 , PHE B:6 , TYR B:144 , ALA B:148 , LEU B:500 , HOH B:2245 , HOH B:2567 , HOH B:2568 , HOH B:2569BINDING SITE FOR RESIDUE MRD B1522
16BC7SOFTWARELEU B:275 , GLN B:279 , HOH B:2570 , HOH B:2571BINDING SITE FOR RESIDUE MRD B1523
17BC8SOFTWARETYR B:38 , TRP B:46 , GLU B:221BINDING SITE FOR RESIDUE MPD B1524
18BC9SOFTWARELEU A:27 , ARG A:28 , TYR A:122 , GLU A:355 , PRO B:353 , GLU B:355 , GLU B:356 , HOH B:2573 , HOH B:2574BINDING SITE FOR RESIDUE MPD B1525
19CC1SOFTWARESER B:55 , LEU B:56 , GLU B:123 , ASP B:211 , HOH B:2132 , HOH B:2420BINDING SITE FOR RESIDUE NA B1526

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J5N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:154 -Pro A:155
2Tyr B:154 -Pro B:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J5N)

(-) Exons   (0, 0)

(no "Exon" information available for 2J5N)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:517
 aligned with Q5SI02_THET8 | Q5SI02 from UniProtKB/TrEMBL  Length:516

    Alignment length:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             516 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     | 
        Q5SI02_THET8      1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF-    -
               SCOP domains d2j5na_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2j5nA01 A:1-289,A:480-516 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                                              2j5nA02 A:290-479 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                   2j5nA01 A:1-289,A:480-516            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh..eee.eee..eee....eeeee.......eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhhhhhh..eeee..............eeee.....hhhhh......eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee................hhhh........hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j5n A    1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERFG 1517
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             516|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1517

Chain B from PDB  Type:PROTEIN  Length:517
 aligned with Q5SI02_THET8 | Q5SI02 from UniProtKB/TrEMBL  Length:516

    Alignment length:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             516 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     | 
        Q5SI02_THET8      1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF-    -
               SCOP domains d2j5nb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2j5nB01 B:1-289,B:480-516 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                                              2j5nB02 B:290-479 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                   2j5nB01 B:1-289,B:480-516            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh...ee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhhhhhhhheeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee................hhhh........hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j5n B    1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERFG 1517
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             516|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1517

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J5N)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SI02_THET8 | Q5SI02)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5SI02_THET8 | Q5SI022bhp 2bhq 2bja 2bjk 2ehq 2ehu 2eii 2eit 2eiw 2ej6 2ejd 2ejl 2iy6 2j40

(-) Related Entries Specified in the PDB File

2bhp CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NAD.
2bhq CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND PRODUCT GLUTAMATE.
2bja CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NADH.
2bjk CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NAD AND CITRATE.
2iy6 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE
2j40 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHILUS WITH BOUND INHIBITOR L- PROLINE AND NAD. RELATED ID: TTK003000033.9 RELATED DB: TARGETDB