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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE HUMAN PROLIDASE WITH GLYPRO 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 :  1.55
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, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2GOL5Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
4PRO2Mod. Amino AcidPROLINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:287 , HIS A:370 , GLU A:412 , GLU A:452 , NA A:500 , GLY A:503binding site for residue NA A 499
02AC2SOFTWAREASP A:276 , ASP A:287 , GLU A:412 , GLU A:452 , NA A:499 , GLY A:503 , PRO A:504binding site for residue NA A 500
03AC3SOFTWARETYR A:241 , ILE A:244 , ASP A:276 , ASP A:287 , HIS A:370 , HIS A:377 , NA A:499 , NA A:500 , PRO A:504 , HOH A:768binding site for residue GLY A 503
04AC4SOFTWARELEU A:254 , HIS A:255 , HIS A:377 , ARG A:398 , GLU A:412 , ARG A:450 , NA A:500 , GLY A:503 , HOH A:801 , HOH A:824binding site for residue PRO A 504
05AC5SOFTWAREPHE A:9 , TRP A:10 , LEU A:11 , LYS A:120 , HOH A:602 , HOH A:611 , HOH A:626 , ASP B:264binding site for residue GOL A 505
06AC6SOFTWAREASP B:287 , HIS B:370 , GLU B:412 , GLU B:452 , NA B:500 , GLY B:503binding site for residue NA B 499
07AC7SOFTWAREASP B:276 , ASP B:287 , GLU B:412 , GLU B:452 , NA B:499 , GLY B:503 , PRO B:504binding site for residue NA B 500
08AC8SOFTWARETYR B:241 , ILE B:244 , ASP B:276 , ASP B:287 , HIS B:370 , HIS B:377 , NA B:499 , NA B:500 , PRO B:504 , HOH B:884binding site for residue GLY B 503
09AC9SOFTWARETRP A:107 , LEU B:254 , HIS B:255 , HIS B:377 , ARG B:398 , GLU B:412 , ARG B:450 , NA B:500 , GLY B:503 , HOH B:734 , HOH B:801binding site for residue PRO B 504
10AD1SOFTWAREALA B:342 , HIS B:343 , LEU B:347 , SER B:348 , HOH B:783binding site for residue GOL B 505
11AD2SOFTWAREHIS A:255 , HIS A:377 , HOH A:1010 , ASP B:60 , THR B:61 , GLY B:62 , HOH B:621 , HOH B:643 , HOH B:674 , HOH B:984binding site for residue GOL B 506
12AD3SOFTWAREASP A:264 , PHE B:9 , TRP B:10 , HOH B:608 , HOH B:610 , HOH B:865binding site for residue GOL B 507
13AD4SOFTWAREGLU B:387 , ARG B:388binding site for residue GOL B 508

(-) 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 5M4J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M4J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M4J)

(-) Exons   (0, 0)

(no "Exon" information available for 5M4J)

(-) 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........eeeee....ee......ee....hhhhhhhhh......eeeee.....eeeee.....hhhhhh....hhhhhhhhhh..eeee..hhhhhhhhhh...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
                 5m4j 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........eehhhhhhhhhhhhhhhhhh.......eeeee....ee......ee....hhhhhhhhh......eeeee.....eeeee.....hhhhhh....hhhhhhhhhh..eeee..hhhhhhhhhh...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
                 5m4j 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
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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 5M4J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M4J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M4J)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5M4J)

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  PEPD_HUMAN | P12955
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  3.4.13.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        PEPD_HUMAN | P12955: 2iw2 2okn 5m4g 5m4l 5m4q

(-) Related Entries Specified in the PDB File

5m4g CONTAINS THE SAME PROTEIN IN "APO" FORM.
5m4l CONTAINS THE SAME PROTEIN IN COMPLEX WITH DIFFERENT SUBSTRATE.
5m4q CONTAINS THE SAME PROTEIN IN COMPLEX WITH PRODUCT.