4BTA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-244) TYPE I FROM HUMAN

Authors :   J. Anantharajan, M. K. Koski, M. Pekkala, R. K. Wierenga

Date :   14 Jun 13 (Deposition) - 09 Oct 13 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Oxidoreductase, Tetratricopeptide Repeat Motif, Coiled-Coil, Proline Rich Peptide (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

Molecule 1 - PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
	Chains	:	A, B
	EC Number	:	1.14.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Expression System Vector Type	:	PLASMID
	Fragment	:	COLLAGEN BINDING DOMAIN, RESIDUES 18-261
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	4-PH ALPHA-1, PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1, PROLYL-4 HYDROXYLASE TYPE I

Molecule 2 - PROLINE RICH PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	9 RESIDUE PEPTIDE- PPGPPGPRPG

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4BTA)

(no "Site" information available for 4BTA)

(no "SS Bond" information available for 4BTA)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:140	-	His A:141
2	Pro C:8	-	Gly C:9

(no "SAP(SNP)/Variant" information available for 4BTA)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	P4HA1_HUMAN	205-238	2	A:188-221 B:188-221
2	TPR_REGION	PS50293	TPR repeat region circular profile.	P4HA1_HUMAN	205-238	2	A:188-221 B:188-221

Asymmetric/Biological Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000394890	1a	ENSE00001372871	chr10:74856732-74856524	209	P4HA1_HUMAN	-	0	0	-	-
1.2b	ENST00000394890	2b	ENSE00001170044	chr10:74834673-74834566	108	P4HA1_HUMAN	1-26	26	2	A:3-9 B:7-9	7 3
1.3	ENST00000394890	3	ENSE00001102025	chr10:74833585-74833489	97	P4HA1_HUMAN	26-58	33	2	A:9-41 B:9-41	33 33
1.4	ENST00000394890	4	ENSE00001102018	chr10:74831938-74831787	152	P4HA1_HUMAN	58-109	52	2	A:41-92 B:41-92	52 52
1.5	ENST00000394890	5	ENSE00000987124	chr10:74828741-74828604	138	P4HA1_HUMAN	109-155	47	2	A:92-138 B:92-133	47 42
1.6	ENST00000394890	6	ENSE00001169998	chr10:74813348-74813109	240	P4HA1_HUMAN	155-235	81	2	A:138-218 B:147-218 (gaps)	81 72
1.7a	ENST00000394890	7a	ENSE00001169991	chr10:74811007-74810811	197	P4HA1_HUMAN	235-300	66	2	A:218-239 B:218-234	22 17
1.8	ENST00000394890	8	ENSE00001169986	chr10:74806859-74806683	177	P4HA1_HUMAN	301-359	59	0	-	-
1.9	ENST00000394890	9	ENSE00001169981	chr10:74804809-74804739	71	P4HA1_HUMAN	360-383	24	0	-	-
1.11b	ENST00000394890	11b	ENSE00001169972	chr10:74790128-74790029	100	P4HA1_HUMAN	383-416	34	0	-	-
1.12a	ENST00000394890	12a	ENSE00001169965	chr10:74776657-74776604	54	P4HA1_HUMAN	417-434	18	0	-	-
1.13	ENST00000394890	13	ENSE00001169956	chr10:74774047-74773982	66	P4HA1_HUMAN	435-456	22	0	-	-
1.14b	ENST00000394890	14b	ENSE00001169951	chr10:74770795-74770727	69	P4HA1_HUMAN	457-479	23	0	-	-
1.15a	ENST00000394890	15a	ENSE00001169944	chr10:74769661-74769565	97	P4HA1_HUMAN	480-512	33	0	-	-
1.16a	ENST00000394890	16a	ENSE00001382372	chr10:74768050-74766982	1069	P4HA1_HUMAN	512-534	23	0	-	-

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:237
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:237
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
          P4HA1_HUMAN    20 GFFTSIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAKEK 256
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. 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) 1.2b   -------------------------------Exon 1.4  PDB: A:41-92 UniProt: 58-109              ---------------------------------------------Exon 1.6  PDB: A:138-218 UniProt: 155-235                                        --------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.3  PDB: A:9-41            --------------------------------------------------Exon 1.5  PDB: A:92-138 UniProt: 109-155       -------------------------------------------------------------------------------Exon 1.7a [INCOMPLETE] Transcript 1 (2)
                 4bta A   3 GFFTSIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMAKEK 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:228
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        
          P4HA1_HUMAN    24 SIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYI 251
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhh-------------hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh----hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh 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:147-218 (gaps) UniProt: 155-235 [INCOMPLETE]                    ---------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.3  PDB: B:9-41            --------------------------------------------------Exon 1.5  PDB: B:92-133 UniProt: 109-155       -------------------------------------------------------------------------------Exon 1.7a         Transcript 1 (2)
                 4bta B   7 SIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISK-------------AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVY----LDKALLLTKKLLELDPEHQRANGNLKYFEYI 234
                                    16        26        36        46        56        66        76        86        96       106       116       126      |  -         -|      156       166       176       186       196  |    206       216       226        
                                                                                                                                                        133           147                                                 199  204

Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4bta C   1 PPGPPGPPG   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 '\|'

(no "SCOP Domain" information available for 4BTA)

(no "CATH Domain" information available for 4BTA)

(no "Pfam Domain" information available for 4BTA)

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4bta)

	Sites
(no "Sites" information available for 4bta)

	Cis Peptide Bonds
		Lys A:140 - His A:141	[ RasMol ]
		Pro C:8 - Gly C:9	[ RasMol ]

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	4bta
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	P4HA1_HUMAN \| P13674
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	1.14.11.2
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	P4HA1_HUMAN \| P13674
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UniProtKB/Swiss-Prot
	P4HA1_HUMAN \| P13674	:	1tjc 2v5f 2yq8 4bt8 4bt9 4btb

4bt8	CRYSTAL STRUCTURE OF THE APO FORM OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL- 4 HYDROXYLASE TYPE I FROM HUMAN
4bt9	CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238 ) TYPE I FROM HUMAN
4btb	CRYSTAL STRUCTURE OF THE PEPTIDE(PRO)9 BOUND COMPLEX OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238) TYPE I FROM HUMAN

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (6, 12)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

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