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(-) Description

Title :  ALGAL PROLYL 4-HYDROXYLASE COMPLEXED WITH ZINC AND (SER-PRO)5 PEPTIDE SUBSTRATE
 
Authors :  M. K. Koski, R. K. Wierenga
Date :  07 Apr 09  (Deposition) - 23 Jun 09  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C,D,X,Y
Biol. Unit 1:  A,B,X  (1x)
Biol. Unit 2:  C,D,Y  (1x)
Keywords :  Jelly-Roll, Double-Stranded Beta-Helix, Proline-Rich Peptide, Poly- (L-Proline) Type Ii Helix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. K. Koski, R. Hieta, M. Hirsila, A. Ronka, J. Myllyharju, R. K. Wierenga
The Crystal Structure Of An Algal Prolyl 4-Hydroxylase Complexed With A Proline-Rich Peptide Reveals A Novel Burie Tripeptide Binding Motif
J. Biol. Chem. V. 284 25290 2009
PubMed-ID: 19553701  |  Reference-DOI: 10.1074/JBC.M109.014050

(-) Compounds

Molecule 1 - PREDICTED PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainORIGAMI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINALLY TRUNCATED CONSTRUCT, RESIDUES 30-251
    GeneP4H-1
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
    StrainWILD TYPE CC125 MT+ 137C
    SynonymPROLYL 4-HYDROXYLASE
 
Molecule 2 - PEPTIDE SUBSTRATE (SER-PRO)5
    ChainsX, Y
    EngineeredYES
    Organism ScientificCHLAMYDOMONAS REINHARDTII
    Organism Taxid3055
    Other DetailsTHIS IS DESIGNED USING THE (SER-PRO)N -REGION OF THE POTENTIAL SUBSTRATE OF CR-P4H-1, NAMELY THE DOMAIN 3 OF THE GP1 PROTEIN OF THE C. REINHARDTII CELL WALL (GENBANK ACCESSION CODE AF309494, FERRIS ET AL. 2001, BIOCHEMISTRY 40:2978-2987).
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDXY
Biological Unit 1 (1x)AB  X 
Biological Unit 2 (1x)  CD Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2ZN14Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:143 , ASP A:145 , HIS A:227 , ACY A:254BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWAREHIS A:135 , ASP A:136 , ASP A:236BINDING SITE FOR RESIDUE ZN A 5
03AC3SOFTWAREGLU A:91 , GLU A:141 , HIS D:157BINDING SITE FOR RESIDUE ZN A 7
04AC4SOFTWAREGLU A:83 , HIS A:148 , HOH A:311 , HIS B:157BINDING SITE FOR RESIDUE ZN A 8
05AC5SOFTWAREHIS A:157 , HOH A:319 , ASP B:64BINDING SITE FOR RESIDUE ZN A 10
06AC6SOFTWAREZN A:1 , TYR A:140 , HIS A:143 , ASP A:145 , HIS A:227 , TRP A:243 , PRO X:6BINDING SITE FOR RESIDUE ACY A 254
07AC7SOFTWAREHIS B:143 , ASP B:145 , HIS B:227 , ACY B:254BINDING SITE FOR RESIDUE ZN B 2
08AC8SOFTWAREHIS B:133 , ASP B:236BINDING SITE FOR RESIDUE ZN B 12
09AC9SOFTWAREACY B:5 , HIS B:148 , HIS D:148BINDING SITE FOR RESIDUE ZN B 14
10BC1SOFTWAREZN B:2 , HIS B:143 , ASP B:145 , HIS B:227 , TRP B:243BINDING SITE FOR RESIDUE ACY B 254
11BC2SOFTWAREZN B:14 , HIS B:143 , TYR B:144 , HIS B:148 , HIS D:143 , TYR D:144 , HIS D:148BINDING SITE FOR RESIDUE ACY B 5
12BC3SOFTWAREHIS C:143 , ASP C:145 , HIS C:227 , ACY C:254BINDING SITE FOR RESIDUE ZN C 3
13BC4SOFTWAREHIS C:135 , ASP C:136 , ASP C:236BINDING SITE FOR RESIDUE ZN C 6
14BC5SOFTWAREGLU C:83 , HIS C:148BINDING SITE FOR RESIDUE ZN C 9
15BC6SOFTWAREHIS C:157 , HOH C:423 , ASP D:64BINDING SITE FOR RESIDUE ZN C 11
16BC7SOFTWAREZN C:3 , TYR C:140 , HIS C:143 , ASP C:145 , HIS C:227 , TRP C:243BINDING SITE FOR RESIDUE ACY C 254
17BC8SOFTWAREHIS D:143 , ASP D:145 , HIS D:227 , ACY D:254BINDING SITE FOR RESIDUE ZN D 4
18BC9SOFTWAREHIS D:133 , HIS D:135 , ASP D:236BINDING SITE FOR RESIDUE ZN D 13
19CC1SOFTWAREZN D:4 , HIS D:143 , ASP D:145 , LEU D:166 , HIS D:227 , TRP D:243 , HOH D:464BINDING SITE FOR RESIDUE ACY D 254

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:195 -A:230
2B:195 -B:230
3C:195 -C:230
4D:195 -D:230

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:48 -Pro A:49
2Ser B:48 -Pro B:49
3Asp B:149 -Pro B:150
4Ser C:48 -Pro C:49
5Ser D:48 -Pro D:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GZE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GZE)

(-) Exons   (0, 0)

(no "Exon" information available for 3GZE)

(-) 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:213
 aligned with A8J7D3_CHLRE | A8J7D3 from UniProtKB/TrEMBL  Length:297

    Alignment length:213
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   
         A8J7D3_CHLRE    38 WRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeee....hhhhhhhhhhhhhhhhee..ee......ee.......eeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeee.....eeee..........hhhhh..eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhheee..eee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gze A  38 WRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with A8J7D3_CHLRE | A8J7D3 from UniProtKB/TrEMBL  Length:297

    Alignment length:214
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246    
         A8J7D3_CHLRE    37 EWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee....hhhhhhhhhhhhhhhh.--------------------.eeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee.----............----......eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhh.ee..eee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gze B  37 EWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMV--------------------TGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHY----KYEPHYDYFHDP----PEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
                                    46        56        66        |-         -        96       106       116       126       | -  |    146   |   156       166       176       186       196       206       216       226       236       246    
                                                                 75                   96                                   134  139        150  155                                                                                               

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with A8J7D3_CHLRE | A8J7D3 from UniProtKB/TrEMBL  Length:297

    Alignment length:213
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   
         A8J7D3_CHLRE    38 WRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeee....hhhhhhhhhhhhhhhhee..ee......ee.......eeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeee....eeee..........hhhhh..eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhheee..eee.eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gze C  38 WRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPIG 250
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   

Chain D from PDB  Type:PROTEIN  Length:182
 aligned with A8J7D3_CHLRE | A8J7D3 from UniProtKB/TrEMBL  Length:297

    Alignment length:213
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246   
         A8J7D3_CHLRE    37 EWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMVKSSVVDNESGKSVDSEIRTSTGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYHDGQKYEPHYDYFHDPVNAGPEHGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee....hhhhhhhhhhhhhhhh.-------------------.eeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeee..----.........--------....eeeeeeee.....ee..eee..............hhhhheee......eeeee........hhhhh.ee..eee...eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gze D  37 EWRGEVVHLSWSPRAFLLKNFLSDEECDYIVEKARPKMV-------------------STGTWFAKGEDSVISKIEKRVAQVTMIPLENHEGLQVLHYH----YEPHYDYFH--------HGGQRVVTMLMYLTTVEEGGETVLPNAEQKVTGDGWSECAKRGLAVKPIKGDALMFYSLKPDGSNDPASLHGSCPTLKGDKWSATKWIHVAPI 249
                                    46        56        66        |-         -        96       106       116       126        |-   |   146 |       -|      166       176       186       196       206       216       226       236       246   
                                                                 75                  95                                     135  140     148      157                                                                                            

Chain X from PDB  Type:PROTEIN  Length:6
 aligned with GP1_CHLRE | Q9FPQ6 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:6
            GP1_CHLRE   363 PSPSPS 368
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3gze X   4 PSPSPS   9

Chain Y from PDB  Type:PROTEIN  Length:8
 aligned with GP1_CHLRE | Q9FPQ6 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:8
            GP1_CHLRE   361 PSPSPSPS 368
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3gze Y   2 PSPSPSPS   9

   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 3GZE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GZE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GZE)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A8J7D3_CHLRE | A8J7D3)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0004656    procollagen-proline 4-dioxygenase activity    Catalysis of the reaction: procollagen L-proline + 2-oxoglutarate + O2 = procollagen trans-4-hydroxy-L-proline + succinate + CO2.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0018401    peptidyl-proline hydroxylation to 4-hydroxy-L-proline    The modification of peptidyl-proline to form 4-hydroxy-L-proline; catalyzed by procollagen-proline,2-oxoglutarate-4-dioxygenase.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.

Chain X,Y   (GP1_CHLRE | Q9FPQ6)
molecular function
    GO:0005199    structural constituent of cell wall    The action of a molecule that contributes to the structural integrity of a cell wall.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

2jig ALGAL PROLYL 4-HYDROXYLASE COMPLEXED WITH ZINC AND PYRIDINE -2,4-DICARBOXYLATE
2jij APO FORM OF ALGAL PROLYL 4-HYDROXYLASE
2v4a SEMET LABELLED APO FORM OF ALGAL PROLYL 4-HYDROXYLASE