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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE HUMAN PROLIDASE WITH MG IONS AND LEUPRO LIGAND
 
Authors :  P. Wilk, M. S. Weiss, U. Mueller, H. Dobbek
Date :  18 Oct 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prolidase, Peptidase, Hydrolysis, Pita-Bread, Metalloenzyme, Hydroxide Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Wilk, M. Uehlein, H. Dobbek, U. Mueller, M. S. Weiss
Substrate Specificity And Reaction Mechanism Of Human Prolidase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - XAA-PRO DIPEPTIDASE
    Chains: A, B
    EC Number: 3.4.13.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Gene: PEPD, PRD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: X-PRO DIPEPTIDASE,IMIDODIPEPTIDASE,PEPTIDASE D,PROLINE DIPEPTIDASE,PROLIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2LEU2Mod. Amino AcidLEUCINE
3MG4Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5OH2Ligand/IonHYDROXIDE ION
6PRO2Mod. Amino AcidPROLINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:287 , HIS A:370 , GLU A:412 , GLU A:452 , MG A:500 , OH A:501 , LEU A:503binding site for residue MG A 499
02AC2SOFTWAREASP A:276 , ASP A:287 , THR A:289 , GLU A:452 , MG A:499 , OH A:501 , LEU A:503binding site for residue MG A 500
03AC3SOFTWAREASP A:276 , ASP A:287 , GLU A:412 , GLU A:452 , MG A:499 , MG A:500 , LEU A:503 , PRO A:504binding site for residue OH A 501
04AC4SOFTWARETYR A:241 , ILE A:244 , HIS A:255 , ASP A:276 , ASP A:287 , HIS A:370 , HIS A:377 , MG A:499 , MG A:500 , OH A:501 , PRO A:504binding site for residue LEU A 503
05AC5SOFTWAREHIS A:255 , HIS A:366 , HIS A:377 , ARG A:398 , GLU A:412 , ARG A:450 , OH A:501 , LEU A:503 , HOH A:827 , HOH A:911 , TRP B:107binding site for residue PRO A 504
06AC6SOFTWAREPHE A:9 , TRP A:10 , LEU A:11 , LYS A:120 , HOH A:610 , HOH A:635 , HOH A:642 , ASP B:264binding site for residue GOL A 506
07AC7SOFTWAREGLU A:387 , ARG A:388 , HOH A:603 , HOH A:740binding site for residue GOL A 507
08AC8SOFTWARESER A:134 , THR A:137 , SER A:138 , GLY A:349 , SER A:350 , VAL A:351 , ASP A:352binding site for residue GOL A 508
09AC9SOFTWAREGLY A:165 , ILE A:166 , SER A:167 , HOH A:613binding site for residue GOL A 509
10AD1SOFTWAREASP B:287 , HIS B:370 , GLU B:412 , GLU B:452 , MG B:500 , OH B:501 , LEU B:503binding site for residue MG B 499
11AD2SOFTWAREASP B:276 , ASP B:287 , THR B:289 , GLU B:452 , MG B:499 , OH B:501 , LEU B:503binding site for residue MG B 500
12AD3SOFTWAREASP B:276 , ASP B:287 , GLU B:412 , GLU B:452 , MG B:499 , MG B:500 , LEU B:503 , PRO B:504binding site for residue OH B 501
13AD4SOFTWARETYR B:241 , ILE B:244 , HIS B:255 , ASP B:276 , ASP B:287 , HIS B:370 , HIS B:377 , MG B:499 , MG B:500 , OH B:501 , PRO B:504binding site for residue LEU B 503
14AD5SOFTWARETRP A:107 , HIS B:255 , HIS B:366 , HIS B:377 , ARG B:398 , GLU B:412 , ARG B:450 , OH B:501 , LEU B:503 , HOH B:697 , HOH B:757binding site for residue PRO B 504
15AD6SOFTWAREALA B:342 , HIS B:343 , LEU B:347 , SER B:348 , HOH B:958binding site for residue GOL B 506
16AD7SOFTWAREGLU B:387 , ARG B:388 , HOH B:900binding site for residue GOL B 507
17AD8SOFTWAREASP A:264 , PHE B:9 , TRP B:10 , LEU B:11 , HOH B:607 , HOH B:617 , HOH B:622 , HOH B:796binding site for residue GOL B 508
18AD9SOFTWARELYS B:211 , MET B:479 , HOH B:729 , HOH B:786 , HOH B:1023 , HOH B:1032binding site for residue NA B 509

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:482 -A:482
2B:482 -B:482

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M4L)

(-) Exons   (0, 0)

(no "Exon" information available for 5M4L)

(-) Sequences/Alignments

Asymmetric/Biological 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:484
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eehhhhhhhhhhhhhhhhh.......eeeeee....ee......ee....hhhhhhhhh......eeeee.....eeeee.....hhhhhh....hhhhhhhhhh..eeee..hhhhhhhhhh..eee...................hhhhh.ee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..ee....eeee.hhhhh..................eeeeee.ee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh............................hhhhh..........eeee..eee.hhhhhhhhhhhhhhhh..hhhhhhhhh...eee..eeeee....eee......hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m4l A   6 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCDKAFTPF 489
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485    


Chain B from PDB  Type:PROTEIN  Length:484
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eehhhhhhhhhhhhhhhhh........eeeee..................hhhhhhhhh......eeeee.....eeeee.....hhhhhh....hhhhhhhhhh..eeee..hhhhhhhhh....ee...................hhhhh.ee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..ee....eeee.hhhhh..................eeeeee.ee.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhh............................hhhhh..........eeee..eee.hhhhhhhhhhhhhhhh..hhhhhhhhh...eee..eeeee....eee......hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m4l B   6 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCDKAFTPF 489
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485
   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  (0, 0)

(no "SCOP Domain" information available for 5M4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M4L)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M4L)

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        PEPD_HUMAN | P12955: 2iw2 2okn 5m4g 5m4j 5m4q

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