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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE PEPTIDE-BINDING DOMAIN OF HUMAN TYPE I COLLAGEN PROLYL 4-HYDROXYLASE.
 
Authors :  M. Pekkala, R. Hieta, K. Kivirikko, J. Myllyharju, R. Wierenga
Date :  06 Oct 08  (Deposition) - 17 Nov 09  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Endoplasmic Reticulum, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Pekkala, R. Hieta, K. Kivirikko, J. Myllyharju, R. Wierenga
Crystal Structure Of Wild Type Peptide-Binding Domain Of Human Type I Collagen Prolyl 4- Hydroxylase.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
    ChainsA
    EC Number1.14.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidALPHA-1F144-S244
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-22B
    FragmentPEPTIDE-SUBSTRATE-BINDING DOMAIN, RESIDUES 161-263
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym4-PH ALPHA-1, PROCOLLAGEN-PROLINE, 2-OXOGLUTARATE-4- DIOXYGENASE SUBUNIT ALPHA-1
 
Molecule 2 - HEXA-HISTIDINE PEPTIDE
    ChainsX
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidALPHA-1F144-S244
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-22B
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2V5F)

(-) Sites  (0, 0)

(no "Site" information available for 2V5F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V5F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V5F)

(-) PROSITE Motifs  (2, 1)

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

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003948901aENSE00001372871chr10:74856732-74856524209P4HA1_HUMAN-00--
1.2bENST000003948902bENSE00001170044chr10:74834673-74834566108P4HA1_HUMAN1-26260--
1.3ENST000003948903ENSE00001102025chr10:74833585-7483348997P4HA1_HUMAN26-58330--
1.4ENST000003948904ENSE00001102018chr10:74831938-74831787152P4HA1_HUMAN58-109520--
1.5ENST000003948905ENSE00000987124chr10:74828741-74828604138P4HA1_HUMAN109-155470--
1.6ENST000003948906ENSE00001169998chr10:74813348-74813109240P4HA1_HUMAN155-235811A:144-21875
1.7aENST000003948907aENSE00001169991chr10:74811007-74810811197P4HA1_HUMAN235-300661A:218-24023
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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:97
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:97
                                   170       180       190       200       210       220       230       240       250       
          P4HA1_HUMAN   161 FLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAKEKD 257
               SCOP domains d2v5fa_ A: automated matches                                                                      SCOP domains
               CATH domains 2v5fA00 A:144-240  [code=1.25.40.10, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. 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) Exon 1.6  PDB: A:144-218 UniProt: 155-235 [INCOMPLETE]                     ---------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.7a [INCOMPLETE]  Transcript 1 (2)
                 2v5f A 144 FLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAKEKD 240
                                   153       163       173       183       193       203       213       223       233       

Chain X from PDB  Type:PROTEIN  Length:6
                                      
               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
                 2v5f X  -1 HHHHHH   4

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V5F)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 2yq8 4bt8 4bt9 4bta 4btb

(-) Related Entries Specified in the PDB File

1tjc CRYSTAL STRUCTURE OF PEPTIDE-SUBSTRATE-BINDING DOMAIN OFHUMAN TYPE I COLLAGEN PROLYL 4- HYDROXYLASE