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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROLIDASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Feb 05  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Prolidase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The Prolidase From Pyrococcus Horikoshii Ot3
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
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: PROLIDASE, X-PRO DIPEPTIDASE, PROLINE DIPEPTIDASE, IMIDODIPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:181 , ASP A:212 , ASP A:223 , HIS A:294 , GLU A:316 , GLU A:330 , ZN A:405 , ZN A:406 , HOH A:1743BINDING SITE FOR RESIDUE CAC A 403
2AC2SOFTWAREPHE B:181 , ASP B:212 , ASP B:223 , VAL B:293 , HIS B:294 , GLU B:316 , GLU B:330 , ZN B:407 , ZN B:408 , HOH B:548BINDING SITE FOR RESIDUE CAC B 404
3AC3SOFTWAREASP A:212 , ASP A:223 , THR A:225 , GLU A:330 , CAC A:403 , ZN A:406BINDING SITE FOR RESIDUE ZN A 405
4AC4SOFTWAREASP A:223 , HIS A:287 , GLU A:316 , GLU A:330 , CAC A:403 , ZN A:405BINDING SITE FOR RESIDUE ZN A 406
5AC5SOFTWAREASP B:212 , ASP B:223 , THR B:225 , GLU B:330 , CAC B:404 , ZN B:408BINDING SITE FOR RESIDUE ZN B 407
6AC6SOFTWAREASP B:223 , HIS B:287 , GLU B:316 , GLU B:330 , CAC B:404 , ZN B:407BINDING SITE FOR RESIDUE ZN B 408
7AC7SOFTWAREHOH A:1424 , HOH A:1518 , HOH A:1613 , HOH A:1647 , HOH A:1746 , HOH A:1747BINDING SITE FOR RESIDUE MG A 1409
8AC8SOFTWARELYS A:27 , ASN A:30 , GLU A:94 , SER A:95 , SER A:96 , ASP A:118 , ARG A:125 , TRP A:296 , GOL A:1402 , HOH A:1491BINDING SITE FOR RESIDUE GOL A 1401
9AC9SOFTWARELYS A:27 , ARG A:125 , GLU A:292 , TRP A:296 , GOL A:1401 , HOH A:1717BINDING SITE FOR RESIDUE GOL A 1402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WY2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:296 -Pro A:297
2Trp B:296 -Pro B:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WY2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROLINE_PEPTIDASEPS00491 Aminopeptidase P and proline dipeptidase signature.PEPQ_PYRHO283-295
 		  2A:283-295
B:283-295

(-) Exons   (0, 0)

(no "Exon" information available for 1WY2)

(-) 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:351
 aligned with PEPQ_PYRHO | O58885 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    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       280       290       300       310       320       330       340       350 
           PEPQ_PYRHO     1 MDIMNEKVKKIIEFMDKNSIDAVLIAKNPNVYYISGASPLAGGYILITGESATLYVPELEYEMAKEESNIPVEKFKKMDEFYKALEGIKSLGIESSLPYGFIEELKKKANIKEFKKVDDVIRDMRIIKSEKEIKIIEKACEIADKAVMAAIEEITEGKKEREVAAKVEYLMKMNGAEKPAFDTIIASGYRSALPHGVASDKRIERGDLVVIDLGALYQHYNSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVESAKPGITAKELDSIARNIIAEYGYGEYFNHSLGHGVGLEVHEWPRVSQYDETVLREGMVITIEPGIYIPKIGGVRIEDTILITKNGSKRLTKTERELI 351
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wy2A01 A:1-125 Creatine Amidinohydrolase, subunit A, domain 1                                                               1wy2A02 A:126-351 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...eeee.hhhhhhhhhh.......eeeee..eeeeeeehhhhhhhhhhh...eeee.hhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeeee..eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wy2 A   1 MDIMNEKVKKIIEFMDKNSIDAVLIAKNPNVYYISGASPLAGGYILITGESATLYVPELEYEMAKEESNIPVEKFKKMDEFYKALEGIKSLGIESSLPYGFIEELKKKANIKEFKKVDDVIRDMRIIKSEKEIKIIEKACEIADKAVMAAIEEITEGKKEREVAAKVEYLMKMNGAEKPAFDTIIASGYRSALPHGVASDKRIERGDLVVIDLGALYQHYNSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVESAKPGITAKELDSIARNIIAEYGYGEYFNHSLGHGVGLEVHEWPRVSQYDETVLREGMVITIEPGIYIPKIGGVRIEDTILITKNGSKRLTKTERELI 351
                                    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       280       290       300       310       320       330       340       350 


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with PEPQ_PYRHO | O58885 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:347
                                    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       274       284       294       304       314       324       334       344       
           PEPQ_PYRHO     5 NEKVKKIIEFMDKNSIDAVLIAKNPNVYYISGASPLAGGYILITGESATLYVPELEYEMAKEESNIPVEKFKKMDEFYKALEGIKSLGIESSLPYGFIEELKKKANIKEFKKVDDVIRDMRIIKSEKEIKIIEKACEIADKAVMAAIEEITEGKKEREVAAKVEYLMKMNGAEKPAFDTIIASGYRSALPHGVASDKRIERGDLVVIDLGALYQHYNSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVESAKPGITAKELDSIARNIIAEYGYGEYFNHSLGHGVGLEVHEWPRVSQYDETVLREGMVITIEPGIYIPKIGGVRIEDTILITKNGSKRLTKTERELI 351
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wy2B01 B:5-125 Creatine Amidinohydrolase, subunit A, domain 1                                                           1wy2B02 B:126-351 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                 CATH domains
           Pfam domains (1) --Creatinase_N-1wy2B01 B:7-127                                                                                             ------Peptidase_M24-1wy2B03 B:134-337                                                                                                                                                                             -------------- Pfam domains (1)
           Pfam domains (2) --Creatinase_N-1wy2B02 B:7-127                                                                                             ------Peptidase_M24-1wy2B04 B:134-337                                                                                                                                                                             -------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh...eeee.hhhhhhhhhh.......eeee....eeeeee..hhhhhhhhh...eeee.hhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI-------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wy2 B   5 NEKVKKIIEFMDKNSIDAVLIAKNPNVYYISGASPLAGGYILITGESATLYVPELEYEMAKEESNIPVEKFKKMDEFYKALEGIKSLGIESSLPYGFIEELKKKANIKEFKKVDDVIRDMRIIKSEKEIKIIEKACEIADKAVMAAIEEITEGKKEREVAAKVEYLMKMNGAEKPAFDTIIASGYRSALPHGVASDKRIERGDLVVIDLGALYQHYNSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVESAKPGITAKELDSIARNIIAEYGYGEYFNHSLGHGVGLEVHEWPRVSQYDETVLREGMVITIEPGIYIPKIGGVRIEDTILITKNGSKRLTKTERELI 351
                                    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       274       284       294       304       314       324       334       344
   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 1WY2)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: AMP_N-like (22)
(-)
Clan: no clan defined [family: Peptidase_M24] (23)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PEPQ_PYRHO | O58885)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0102009    proline dipeptidase activity    Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal <=> L-proline + a standard alpha amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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