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(-) Description

Title :  STRUCTURE OF HUMAN PYCR-1 COMPLEXED WITH PROLINE
 
Authors :  J. J. Tanner
Date :  20 Dec 16  (Deposition) - 15 Mar 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1PRO10Mod. Amino AcidPROLINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 28)
No.NameCountTypeFull Name
1PRO20Mod. Amino AcidPROLINE
2SO48Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1PRO4Mod. Amino AcidPROLINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1PRO4Mod. Amino AcidPROLINE
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1PRO4Mod. Amino AcidPROLINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:231 , SER A:233 , GLY A:236 , ALA A:237 , THR A:238 , HOH A:525 , THR B:171 , GLY B:175binding site for residue PRO A 401
02AC2SOFTWAREALA A:136 , THR A:137 , GLU A:163 , GLU A:164 , HOH A:502 , HOH A:541binding site for residue PRO A 402
03AC3SOFTWARETHR A:171 , GLY A:175 , VAL B:231 , SER B:233 , GLY B:236 , ALA B:237 , THR B:238 , HOH B:517 , HOH B:541binding site for residue PRO B 401
04AC4SOFTWARETHR B:137 , GLU B:163 , GLU B:164 , HOH B:513binding site for residue PRO B 402
05AC5SOFTWAREGLY B:9 , GLN B:10 , LEU B:11 , ALA B:69binding site for residue SO4 B 403
06AC6SOFTWAREVAL C:231 , SER C:233 , GLY C:236 , ALA C:237 , THR C:238 , HOH C:521 , THR D:171binding site for residue PRO C 401
07AC7SOFTWARETHR C:137 , GLU C:163 , GLU C:164 , HOH C:501 , HOH C:505 , HOH C:548binding site for residue PRO C 402
08AC8SOFTWAREGLY C:9 , GLN C:10 , LEU C:11binding site for residue SO4 C 403
09AC9SOFTWARETHR C:171 , GLY C:175 , VAL D:231 , SER D:233 , GLY D:236 , ALA D:237 , THR D:238 , HOH D:523binding site for residue PRO D 401
10AD1SOFTWARETHR D:137 , GLU D:163 , GLU D:164 , HOH D:507binding site for residue PRO D 402
11AD2SOFTWAREGLY D:9 , GLN D:10 , LEU D:11binding site for residue SO4 D 403
12AD3SOFTWARETHR E:171 , GLY E:175 , VAL E:231 , SER E:233 , GLY E:236 , ALA E:237 , THR E:238 , HOH E:526binding site for residue PRO E 401
13AD4SOFTWARETHR E:137 , GLU E:163 , GLU E:164 , HOH E:502 , HOH E:538binding site for residue PRO E 402
14AD5SOFTWAREGLY E:9 , GLN E:10 , LEU E:11binding site for residue SO4 E 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UAU)

(-) 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:276
                                                                                                                                                                                                                                                                                                                    
               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......eeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uau A   1 MSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQPP 402
                                    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   || 
                                                                                                                                                                                                                                                                                                           274| 
                                                                                                                                                                                                                                                                                                            401 


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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uau B  -2 FQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQPP 402
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267      || 
                                                                                                                                                                                                                                                                                                              274| 
                                                                                                                                                                                                                                                                                                               401 


Chain C from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh......eeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uau C   0 SMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMTVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQPP 402
                                     9        19        29       |42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 || 
                                                                37|                                                                                                                                                                                                                                      274| 
                                                                 41                                                                                                                                                                                                                                       401 


Chain D from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uau D   1 MSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEPP 402
                                    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    || 
                                                                                                                                                                                                                                                                                                            275| 
                                                                                                                                                                                                                                                                                                             401 


Chain E from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhh...hhh.eeee..........eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh......eeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uau E   1 MSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMLRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQPP 402
                                    10        20        30      ||47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267      || 
                                                               37|                                                                                                                                                                                                                                  274| 
                                                                45                                                                                                                                                                                                                                   401
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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  5uau
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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 5uat 5uav 5uaw 5uax

(-) Related Entries Specified in the PDB File

5uat 5uav 5uaw 5uax