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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SEMET-LABELED N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF ALPHA SUBUNIT OF PROLYL-4 HYDROXYLASE TYPE I FROM HUMAN.
 
Authors :  J. Anantharajan, M. K. Koski, R. K. Wierenga
Date :  06 Nov 12  (Deposition) - 09 Oct 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Anantharajan, M. K. Koski, P. Kursula, R. Hieta, U. Bergmann, J. Myllyharju, R. K. Wierenga
The Structural Motifs For Substrate Binding And Dimerization Of The Alpha Subunit Of Collagen Prolyl 4-Hydroxylase
Structure V. 21 2107 2013
PubMed-ID: 24207127  |  Reference-DOI: 10.1016/J.STR.2013.09.005

(-) Compounds

Molecule 1 - PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
    ChainsA, B
    EC Number1.14.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainB834
    Expression System Taxid562
    Expression System VectorPET22B
    Expression System Vector TypePLASMID
    FragmentCOLLAGEN BINDING DOMAIN, RESIDUES 18-255
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym4-PH ALPHA-1, PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1, PROLYL-4 HYDROXYLASE TYPE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YQ8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YQ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YQ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YQ8)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.P4HA1_HUMAN205-238
 
  2A:188-221
B:188-221
2TPR_REGIONPS50293 TPR repeat region circular profile.P4HA1_HUMAN205-238
 
  2A:188-221
B:188-221

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003948901aENSE00001372871chr10:74856732-74856524209P4HA1_HUMAN-00--
1.2bENST000003948902bENSE00001170044chr10:74834673-74834566108P4HA1_HUMAN1-26262A:7-9
B:7-9
3
3
1.3ENST000003948903ENSE00001102025chr10:74833585-7483348997P4HA1_HUMAN26-58332A:9-41
B:9-41
33
33
1.4ENST000003948904ENSE00001102018chr10:74831938-74831787152P4HA1_HUMAN58-109522A:41-92
B:41-92
52
52
1.5ENST000003948905ENSE00000987124chr10:74828741-74828604138P4HA1_HUMAN109-155472A:92-137
B:92-137
46
46
1.6ENST000003948906ENSE00001169998chr10:74813348-74813109240P4HA1_HUMAN155-235812A:144-218
B:143-218
75
76
1.7aENST000003948907aENSE00001169991chr10:74811007-74810811197P4HA1_HUMAN235-300662A:218-237
B:218-237
20
20
1.8ENST000003948908ENSE00001169986chr10:74806859-74806683177P4HA1_HUMAN301-359590--
1.9ENST000003948909ENSE00001169981chr10:74804809-7480473971P4HA1_HUMAN360-383240--
1.11bENST0000039489011bENSE00001169972chr10:74790128-74790029100P4HA1_HUMAN383-416340--
1.12aENST0000039489012aENSE00001169965chr10:74776657-7477660454P4HA1_HUMAN417-434180--
1.13ENST0000039489013ENSE00001169956chr10:74774047-7477398266P4HA1_HUMAN435-456220--
1.14bENST0000039489014bENSE00001169951chr10:74770795-7477072769P4HA1_HUMAN457-479230--
1.15aENST0000039489015aENSE00001169944chr10:74769661-7476956597P4HA1_HUMAN480-512330--
1.16aENST0000039489016aENSE00001382372chr10:74768050-747669821069P4HA1_HUMAN512-534230--

(-) 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:225
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:231
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253 
          P4HA1_HUMAN    24 SIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAK 254
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhh....------..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR  PDB: A:188-221               ---------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR_REGION  PDB: A:188-221        ---------------- PROSITE (2)
           Transcript 1 (1) 1.2-------------------------------Exon 1.4  PDB: A:41-92 UniProt: 58-109              ---------------------------------------------Exon 1.6  PDB: A:144-218 UniProt: 155-235 [INCOMPLETE]                           ------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.3  PDB: A:9-41            --------------------------------------------------Exon 1.5  PDB: A:92-137 UniProt: 109-155       -------------------------------------------------------------------------------Exon 1.7a            Transcript 1 (2)
                 2yq8 A   7 SIGQmTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLmKRLNTEWSELENLVLKDmSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLP------FLTAEDCFELGKVAYTEADYYHTELWmEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYImAK 237
                                |   16        26        36        46        56        66    |   76        86  |     96       106       116       126       136|      146       156       166   |   176       186       196       206       216       226       236 
                                |                                                          71-MSE            89-MSE                                         137    144                       170-MSE                                                          235-MSE
                               11-MSE                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:231
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253 
          P4HA1_HUMAN    24 SIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAK 254
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhh....-----...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR  PDB: B:188-221               ---------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR_REGION  PDB: B:188-221        ---------------- PROSITE (2)
           Transcript 1 (1) 1.2-------------------------------Exon 1.4  PDB: B:41-92 UniProt: 58-109              ---------------------------------------------Exon 1.6  PDB: B:143-218 UniProt: 155-235 [INCOMPLETE]                           ------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.3  PDB: B:9-41            --------------------------------------------------Exon 1.5  PDB: B:92-137 UniProt: 109-155       -------------------------------------------------------------------------------Exon 1.7a            Transcript 1 (2)
                 2yq8 B   7 SIGQmTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLmKRLNTEWSELENLVLKDmSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLP-----SFLTAEDCFELGKVAYTEADYYHTELWmEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYImAK 237
                                |   16        26        36        46        56        66    |   76        86  |     96       106       116       126       136|     |146       156       166   |   176       186       196       206       216       226       236 
                               11-MSE                                                      71-MSE            89-MSE                                         137   143                        170-MSE                                                          235-MSE

   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 2YQ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YQ8)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P4HA1_HUMAN | P13674)
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:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is 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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016222    procollagen-proline 4-dioxygenase complex    A protein complex that catalyzes the formation of procollagen trans-4-hydroxy-L-proline and succinate from procollagen L-proline and 2-oxoglutarate, requiring Fe2+ and ascorbate. Contains two alpha subunits that contribute to most parts of the catalytic sites, and two beta subunits that are identical to protein-disulfide isomerase.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P4HA1_HUMAN | P136741tjc 2v5f 4bt8 4bt9 4bta 4btb

(-) Related Entries Specified in the PDB File

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