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(-) Description

Title :  STRUCTURE OF HUMAN PYCR-1 COMPLEXED WITH NADPH
 
Authors :  J. J. Tanner
Date :  20 Dec 16  (Deposition) - 15 Mar 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E  (2x)
Keywords :  Amino-Acid Biosynthesis, Oxidoreductase, Proline Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Christensen, S. M. Patel, D. A. Korasick, A. C. Campbell, K. L. Krause, D. F. Becker, J. J. Tanner
Resolving The Cofactor-Binding Site In The Proline Biosynthetic Enzyme Human Pyrroline-5-Carboxylate Reductase 1.
J. Biol. Chem. V. 292 7233 2017
PubMed-ID: 28258219  |  Reference-DOI: 10.1074/JBC.M117.780288

(-) Compounds

Molecule 1 - PYRROLINE-5-CARBOXYLATE REDUCTASE 1, MITOCHONDRIAL
    Chains: A, B, C, D, E
    EC Number: 1.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-300
    Gene: PYCR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: P5CR 1

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE
Biological Unit 2 (1x): AB   
Biological Unit 3 (1x):   CD 
Biological Unit 4 (2x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3SO48Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NDP-1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:231 , SER A:233 , GLY A:236 , ALA A:237 , THR A:238 , HOH A:503 , HOH A:513 , HOH A:518 , HOH A:524binding site for residue SO4 A 401
2AC2SOFTWAREALA A:97 , VAL B:231 , SER B:233 , GLY B:236 , ALA B:237 , THR B:238 , HOH B:504 , HOH B:512 , HOH B:536 , HOH B:547 , HOH B:552 , HOH B:575binding site for residue SO4 B 401
3AC3SOFTWAREGLY C:7 , ALA C:8 , GLY C:9 , GLN C:10 , LEU C:11 , SER C:34 , PRO C:35 , ASP C:36 , MET C:37 , ASN C:56 , ALA C:69 , VAL C:70 , LYS C:71 , PRO C:72 , ILE C:78 , CYS C:95 , ALA C:96 , ALA C:97 , MET C:121 , THR C:122 , THR C:124 , HOH C:515 , HOH C:527 , HOH C:536 , HOH C:543 , HOH C:553 , HOH C:556 , HOH C:565 , HOH C:574 , HOH C:589 , ASN D:230 , VAL D:231 , SO4 D:401binding site for residue NDP C 401
4AC4SOFTWAREVAL C:231 , SER C:233 , GLY C:236 , ALA C:237 , THR C:238 , HOH C:503 , HOH C:546 , HOH C:579binding site for residue SO4 C 402
5AC5SOFTWAREASP B:64 , ARG B:89binding site for residue PEG C 403
6AC6SOFTWARENDP C:401 , VAL D:231 , SER D:233 , ALA D:237 , THR D:238 , HOH D:532 , HOH D:556binding site for residue SO4 D 401
7AC7SOFTWAREALA E:8 , GLY E:9 , GLN E:10 , LEU E:11 , SER E:34 , PRO E:35 , ASP E:36 , MET E:37 , ASN E:56 , ALA E:69 , VAL E:70 , LYS E:71 , PRO E:72 , ILE E:78 , CYS E:95 , ALA E:96 , ALA E:97 , MET E:121 , THR E:122 , THR E:124 , ASN E:230 , VAL E:231 , HOH E:503 , HOH E:508 , HOH E:519 , HOH E:551 , HOH E:556 , HOH E:559 , HOH E:572binding site for residue NDP E 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UAT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UAT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UAT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UAT)

(-) Exons   (0, 0)

(no "Exon" information available for 5UAT)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhh...hhh.eee..hhhhhhhh.ee..hhhhhhhhh.eeee.....hhhhhhhhhhhhh....eeee.....hhhhhhhhhhh......eeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uat A   1 MSVGFILAFALAKGFTAAGVLAAHKIMASTVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQ 274
                                 || 14        24        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
                                 6|                    33|                                                                                                                                                                                                                                         
                                 11                     41                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uat B  -5 NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264         


Chain C from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uat C  -3 YFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       


Chain D from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uat D  -5 NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264         


Chain E from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uat E   0 SMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQ 274
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 5UAT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UAT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UAT)

(-) Gene Ontology  (13, 13)

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  P5CR1_HUMAN | P32322
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  1.5.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        P5CR1_HUMAN | P32322: 2ger 2gr9 2gra 2izz 5uau 5uav 5uaw 5uax

(-) Related Entries Specified in the PDB File

5uau 5uav 5uaw 5uax