1Y56 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L-PROLINE DEHYDROGENASE FROM P.HORIKOSHII

Authors :   H. Tsuge, R. Kawakami, H. Sakuraba, H. Ago, M. Miyano, K. Aki, N. Katunum T. Ohshima

Date :   02 Dec 04 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.86

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)

Keywords :   Dehydrogenase, Protein-Protein Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Tsuge, R. Kawakami, H. Sakuraba, H. Ago, M. Miyano, K. Aki, N. Katunuma, T. Ohshima
Crystal Structure Of A Novel Fad-, Fmn-, And Atp-Containing L-Proline Dehydrogenase Complex From Pyrococcus Horikoshii
J. Biol. Chem. V. 280 31045 2005
PubMed-ID: 16027125 | Reference-DOI: 10.1074/JBC.C500234200

Molecule 1 - HYPOTHETICAL PROTEIN PH1363
	Chains	:	A
	EC Number	:	1.5.99.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21 CODONPLUS RIL(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	L-PROLINE DEHYDROGENASE ALPHA SUBUNIT

Molecule 2 - SARCOSINE OXIDASE
	Chains	:	B
	EC Number	:	1.5.99.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21 CODONPLUS RIL(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	L-PROLINE DEHYDROGENASE BETA SUBUNIT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 7)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	CXS	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
4	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	FE	1	Ligand/Ion	FE (III) ION
6	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
7	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 20)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CXS	4	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
4	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	FE	-1	Ligand/Ion	FE (III) ION
6	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
7	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CXS	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
4	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	FE	-1	Ligand/Ion	FE (III) ION
6	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
7	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 4)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CXS	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
4	FAD	-1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	FE	-1	Ligand/Ion	FE (III) ION
6	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
7	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CXS	-1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
4	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	FE	-1	Ligand/Ion	FE (III) ION
6	FMN	-1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
7	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:445 , GLN A:448	BINDING SITE FOR RESIDUE FE A 805
2	AC2	SOFTWARE	ASN B:202 , TYR B:308 , ALA B:309 , SER B:334 , GLY B:335 , FAD B:800	BINDING SITE FOR RESIDUE CL B 804
3	AC3	SOFTWARE	ILE A:430 , THR A:431 , ASP A:432 , ILE A:435 , TYR B:169	BINDING SITE FOR RESIDUE SO4 A 806
4	AC4	SOFTWARE	GLY B:12 , GLY B:14 , ILE B:15 , VAL B:16 , ILE B:34 , GLU B:35 , LYS B:36 , SER B:41 , SER B:43 , THR B:44 , ARG B:46 , CYS B:47 , GLY B:48 , THR B:49 , GLY B:50 , GLU B:171 , VAL B:172 , ALA B:200 , THR B:201 , ASN B:202 , TRP B:204 , ILE B:208 , TYR B:251 , GLY B:306 , TYR B:307 , TYR B:308 , GLY B:335 , HIS B:336 , GLY B:337 , PHE B:338 , MET B:339 , CL B:804 , HOH B:808 , HOH B:809 , HOH B:816 , HOH B:822	BINDING SITE FOR RESIDUE FAD B 800
5	AC5	SOFTWARE	LYS A:437 , ARG A:438 , HIS A:441 , MET A:444 , GLN A:448 , ARG A:477 , HOH A:885 , PHE B:45 , ARG B:46 , CYS B:47 , ARG B:302 , TRP B:304	BINDING SITE FOR RESIDUE FMN A 802
6	AC6	SOFTWARE	GLY A:113 , GLY A:115 , PRO A:116 , ALA A:117 , GLU A:135 , GLU A:136 , ARG A:137 , GLY A:142 , ASP A:143 , THR A:179 , ALA A:181 , ALA A:212 , THR A:213 , GLY A:214 , ARG A:309 , GLY A:348 , SER A:349 , HIS A:356 , ASN A:359 , ILE A:480 , HOH A:811 , HOH A:822 , HOH A:866	BINDING SITE FOR RESIDUE ATP A 801
7	AC7	SOFTWARE	GLY A:138 , TRP A:139 , VAL A:242 , TRP A:243 , GLU A:244	BINDING SITE FOR RESIDUE CXS A 803

Asymmetric Unit

No.	Residues
1	A:413	-	A:452

Asymmetric Unit

No.	Residues
1	Gly B:50	-	Ile B:51

(no "SAP(SNP)/Variant" information available for 1Y56)

(no "PROSITE Motif" information available for 1Y56)

(no "Exon" information available for 1Y56)

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:484
 aligned with O59088_PYRHO | O59088 from UniProtKB/TrEMBL  Length:493

    Alignment length:490
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
         O59088_PYRHO     3 MRPLDLTEKRGKKVTIYFEGKELEAYEGEKLPVALLANEIYWLTTSNEGRKRGAFTFGPVPMTVNGVKGLEARRIKVKDGMKIERQGYYDFHEEPVVEPGEIERVVVDVAIIGGGPAGIGAALELQQYLTVALIEERGWLGGDMWLKGIKQEGFNKDSRKVVEELVGKLNENTKIYLETSALGVFDKGEYFLVPVVRGDKLIEILAKRVVLATGAIDSTMLFENNDMPGVFRRDFALEVMNVWEVAPGRKVAVTGSKADEVIQELERWGIDYVHIPNVKRVEGNEKVERVIDMNNHEYKVDALIFADGRRPDINPITQAGGKLRFRRGYYSPVLDEYHRIKDGIYVAGSAVSIKPHYANYLEGKLVGAYILKEFGYDAQPCIYEEKLREYEPESLSIPRIPLDKFNLEDVQICGCDVSLKKVDEVIRKGITDLQIIKRLTHLAMGFCQGRYCLFNGAVVVSQRTGKKLSEIDLPVARSPIKNVKMGILAR 492
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Fer2_4-1y56A01 A:11-88                                                        -------------------Pyr_redox_2-1y56A02 A:108-355                                                                                                                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee..eeeeee...hhhhhhhhh.....ee.....ee........ee.......ee.hhh......ee...........------..eeeee...ee..hhhhhhhhhhhh....eeee........hhhhh..ee....eehhhhhhhhhhh....eeee..eee...ee....eeeeeee..eeeeeee..eee...eee............eeehhhhhhhhhh.......eeeee..hhhhhhhhhhhhh.eeee...eeeee......eeee....eee..eeee...eee.hhhhhhh...eeee..eeee......eee..eee........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.............................hhhhhhhhhhh...hhhhhhhhh...........hhhhhhhhhhhhhh.hhhhh...........ee.hhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y56 A   1 MRPLDLTEKRGKKVTIYFEGKELEAYEGEKLPVALLANEIYWLTTSNEGRKRGAFTFGPVPMTVNGVKGLEARRIKVKDGMKIERQGYYDFHEE------EIERVVVDVAIIGGGPAGIGAALELQQYLTVALIEERGWLGGDMWLKGIKQEGFNKDSRKVVEELVGKLNENTKIYLETSALGVFDKGEYFLVPVVRGDKLIEILAKRVVLATGAIDSTMLFENNDMPGVFRRDFALEVMNVWEVAPGRKVAVTGSKADEVIQELERWGIDYVHIPNVKRVEGNEKVERVIDMNNHEYKVDALIFADGRRPDINPITQAGGKLRFRRGYYSPVLDEYHRIKDGIYVAGSAVSIKPHYANYLEGKLVGAYILKEFGYDAQPCIYEEKLREYEPESLSIPRIPLDKFNLEDVQICGCDVSLKKVDEVIRKGITDLQIIKRLTHLAMGFCQGRYCLFNGAVVVSQRTGKKLSEIDLPVARSPIKNVKMGILAR 490
                                    10        20        30        40        50        60        70        80        90   |     -|      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       360       370       380       390       400       410       420       430       440       450       460       470       480       490
                                                                                                                        94    101

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with O59089_PYRHO | O59089 from UniProtKB/TrEMBL  Length:382

    Alignment length:374
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371    
         O59089_PYRHO     2 LPEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANVRVMKRSVELWKKYSEEYGFSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPEEAKEIVPLLDISEVIAASWNPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGFLIENNEIKGVKTNKGIIKTGIVVNATNAWANLINAMAGIKTKIPIEPYKHQAVITQPIKRGTINPMVISFKYGHAYLTQTFHGGIIGGIGYEIGPTYDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAGYYAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPYRFERGELR 375
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhh...eeee.......hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...ee...eeeee.hhhhhhhhhhhhhhhhhh....eeehhhhhhhh..........eeeee....eehhhhhhhhhhhhhhhh..eee....eeeeee....eeeeee..eeee..eeee.hhhhhhhhhhhhh.......eeeeeeeeee..........eeee.....eeee.......eee.............hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee......eeeee.....eeeee....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y56 B   2 LPEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANVRVMKRSVELWKKYSEEYGFSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPEEAKEIVPLLDISEVIAASWNPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGFLIENNEIKGVKTNKGIIKTGIVVNATNAWANLINAMAGIKTKIPIEPYKHQAVITQPIKRGTINPMVISFKYGHAYLTQTFHGGIIGGIGYEIGPTYDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAGYYAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPYRFERGELR 375
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371

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 1Y56)

(no "CATH Domain" information available for 1Y56)

Asymmetric Unit(hide GO term definitions)

Chain A (O59088_PYRHO | O59088)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
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.

Chain B (O59089_PYRHO | O59089)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly B:50 - Ile B:51	[ RasMol ]

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	1y56
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	O59088_PYRHO \| O59088
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	O59089_PYRHO \| O59089
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	1.5.99.8
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(no "Entries Sharing at Least One Protein Chain" available for 1Y56)

(no "Related Entries Specified in the PDB File" available for 1Y56)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 7)

Sites (7, 7)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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