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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE HUMAN PROLIDASE WITH MN IONS AND PRO 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 :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prolidase, Peptidase, Hydrolysis, Pita-Bread, Metalloenzyme, 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  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2MN4Ligand/IonMANGANESE (II) ION
3OH2Ligand/IonHYDROXIDE ION
4PRO2Mod. Amino AcidPROLINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:287 , HIS A:370 , GLU A:412 , GLU A:452 , MN A:500 , OH A:501 , HOH A:619binding site for residue MN A 499
02AC2SOFTWAREASP A:276 , ASP A:287 , THR A:289 , GLU A:452 , MN A:499 , OH A:501 , HOH A:877binding site for residue MN A 500
03AC3SOFTWAREASP A:276 , ASP A:287 , GLU A:412 , GLU A:452 , MN A:499 , MN A:500 , PRO A:504 , HOH A:619 , HOH A:877binding site for residue OH A 501
04AC4SOFTWAREHIS A:255 , HIS A:366 , HIS A:377 , ARG A:398 , GLU A:412 , OH A:501 , HOH A:619 , HOH A:702 , HOH A:734 , TRP B:107binding site for residue PRO A 504
05AC5SOFTWAREPHE A:9 , TRP A:10 , HOH A:603 , HOH A:621 , ASP B:264binding site for residue GOL A 505
06AC6SOFTWAREHIS A:330 , ARG A:331 , ASP A:334 , HIS A:358 , GLU A:391 , PRO A:392 , LEU A:394 , HOH A:602 , HOH A:605binding site for residue GOL A 506
07AC7SOFTWARETHR A:152 , GLU A:387 , ARG A:388 , HOH A:715binding site for residue GOL A 507
08AC8SOFTWAREALA A:342 , HIS A:343 , LEU A:347 , SER A:348 , HOH A:676binding site for residue GOL A 508
09AC9SOFTWAREASP B:287 , HIS B:370 , GLU B:412 , GLU B:452 , MN B:500 , OH B:501 , HOH B:631binding site for residue MN B 499
10AD1SOFTWAREASP B:276 , ASP B:287 , THR B:289 , GLU B:452 , MN B:499 , OH B:501 , HOH B:871binding site for residue MN B 500
11AD2SOFTWAREASP B:276 , ASP B:287 , GLU B:412 , GLU B:452 , MN B:499 , MN B:500 , PRO B:504 , HOH B:631 , HOH B:871binding site for residue OH B 501
12AD3SOFTWARETRP A:107 , HIS B:255 , HIS B:366 , HIS B:377 , ARG B:398 , GLU B:412 , OH B:501 , HOH B:631 , HOH B:754 , HOH B:800binding site for residue PRO B 504
13AD4SOFTWAREASP A:264 , PHE B:9 , TRP B:10 , LEU B:11 , LYS B:120 , HOH B:674 , HOH B:752 , HOH B:757 , HOH B:965binding site for residue GOL B 505
14AD5SOFTWAREASP B:164 , GLY B:165 , ILE B:166 , SER B:167 , HOH B:662binding site for residue GOL B 506
15AD6SOFTWAREGLU A:227 , HIS A:228 , TYR A:231 , HOH A:895 , SER B:224 , GLU B:227 , HIS B:228 , HOH B:632 , HOH B:819 , HOH B:834binding site for residue GOL B 507

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:58 -B:158
2A:158 -B:58
3A:482 -A:482
4B:482 -B:482

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5M4Q)

(-) 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........eehhhhhhhhhhhhhhhhhh......eeeeee....ee......ee....hhhhhhhhh......eeeee.....eeeee.....hhhhhh....hhhhhhhhhh..eeee..hhhhhhhhhh..eee...ee......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
                 5m4q 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:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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...ee......ee......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
                 5m4q B   6 GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMAGCD 483
                                    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
   Legend:   → Mismatch (orange background)
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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 5M4Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M4Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M4Q)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M4Q)

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        PEPD_HUMAN | P12955: 2iw2 2okn 5m4g 5m4j 5m4l

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