4JY3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE, 5-PYRIDOXIC ACID BOUND FORM

Authors :   J. Kobayashi, H. Yoshida, S. Kamitori, H. Hayashi, K. Mizutani, N. Taka B. Mikami, T. Yagi

Date :   29 Mar 13 (Deposition) - 02 Apr 14 (Release) - 02 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

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

Keywords :   Flavoenzyme, Fad Binding Motif, Oxidoreductase, 3-Hydroxypyridine-5- Carboxylic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kobayashi, H. Yoshida, S. Kamitori, H. Hayashi, K. Mizutani, N. Takahashi, B. Mikami, T. Yagi
Crystal Structure Of 2-Methyl-3-Hydroxypyridine-5-Carboxyli Acid Oxygenase
To Be Published
PubMed: search

Molecule 1 - 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE
	Chains	:	A, B
	EC Number	:	1.14.12.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MLR6788
	Organism Scientific	:	MESORHIZOBIUM LOTI
	Organism Taxid	:	266835
	Strain	:	MAFF303099

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	5PR	2	Ligand/Ion	5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	5PR	1	Ligand/Ion	5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 2 (5, 8)

No.	Name	Count	Type	Full Name
1	5PR	1	Ligand/Ion	5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:18 , GLY A:19 , GLY A:20 , PHE A:21 , ALA A:22 , HIS A:40 , GLU A:41 , LYS A:42 , ILE A:53 , TYR A:54 , ARG A:106 , SER A:128 , GLU A:129 , ALA A:130 , ALA A:155 , ASP A:156 , GLY A:157 , LEU A:179 , ARG A:181 , GLY A:287 , ASP A:288 , ALA A:298 , GLY A:300 , ALA A:301 , GLY A:302 , 5PR A:403 , HOH A:501 , HOH A:502 , HOH A:503 , HOH A:504 , HOH A:542 , HOH A:584 , HOH A:660 , HOH A:687 , HOH A:702 , HOH A:735 , HOH A:787 , HOH A:821	BINDING SITE FOR RESIDUE FAD A 401
02	AC2	SOFTWARE	TRP A:173 , TYR A:270 , CYS A:294	BINDING SITE FOR RESIDUE BME A 402
03	AC3	SOFTWARE	TYR A:54 , LEU A:179 , ARG A:211 , LEU A:213 , TYR A:223 , MET A:227 , TYR A:270 , PRO A:295 , ALA A:296 , ALA A:298 , LEU A:352 , FAD A:401 , HOH A:606 , HOH A:608 , HOH A:628 , HOH A:631 , HOH A:702 , HOH A:959	BINDING SITE FOR RESIDUE 5PR A 403
04	AC4	SOFTWARE	LEU A:73 , GLN A:74 , GLY A:75 , SER A:76 , ASN A:97 , ARG A:102 , PRO A:378 , HOH A:561 , HOH A:566 , HOH A:720 , HOH A:899	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	THR A:95 , PHE A:96 , ASN A:97 , HOH A:520 , HOH A:581 , HOH A:705 , HOH A:712	BINDING SITE FOR RESIDUE GOL A 405
06	AC6	SOFTWARE	LYS A:42 , ASN A:127 , GLU A:129 , GLN A:142 , THR A:143 , HOH A:558	BINDING SITE FOR RESIDUE GOL A 406
07	AC7	SOFTWARE	GLU A:364 , ARG A:367 , TYR A:375	BINDING SITE FOR RESIDUE GOL A 407
08	AC8	SOFTWARE	GLY B:18 , GLY B:19 , GLY B:20 , PHE B:21 , ALA B:22 , HIS B:40 , GLU B:41 , LYS B:42 , ILE B:53 , TYR B:54 , ARG B:106 , SER B:128 , GLU B:129 , ALA B:130 , ALA B:155 , ASP B:156 , GLY B:157 , LEU B:179 , ARG B:181 , GLY B:287 , ASP B:288 , ALA B:298 , GLY B:300 , ALA B:301 , GLY B:302 , 5PR B:403 , HOH B:502 , HOH B:503 , HOH B:505 , HOH B:520 , HOH B:614 , HOH B:657 , HOH B:701 , HOH B:718 , HOH B:733 , HOH B:802 , HOH B:859	BINDING SITE FOR RESIDUE FAD B 401
09	AC9	SOFTWARE	TRP B:173 , TYR B:270 , CYS B:294 , ALA B:347 , EDO B:408	BINDING SITE FOR RESIDUE BME B 402
10	BC1	SOFTWARE	TYR B:54 , LEU B:179 , ARG B:211 , LEU B:213 , TYR B:223 , PRO B:295 , ALA B:296 , ALA B:298 , LEU B:352 , FAD B:401 , HOH B:552 , HOH B:582 , HOH B:664 , HOH B:735 , HOH B:859 , HOH B:965	BINDING SITE FOR RESIDUE 5PR B 403
11	BC2	SOFTWARE	LEU B:73 , GLN B:74 , GLY B:75 , SER B:76 , ASN B:97 , ARG B:102 , PRO B:378 , HOH B:596 , HOH B:612 , HOH B:744 , HOH B:825 , HOH B:947	BINDING SITE FOR RESIDUE GOL B 404
12	BC3	SOFTWARE	THR B:279 , GLY B:281 , VAL B:326 , HOH B:514 , HOH B:750	BINDING SITE FOR RESIDUE GOL B 405
13	BC4	SOFTWARE	LYS B:42 , ASN B:127 , GLU B:129 , GLN B:142 , THR B:143 , HOH B:611 , HOH B:850 , HOH B:852 , HOH B:853	BINDING SITE FOR RESIDUE GOL B 406
14	BC5	SOFTWARE	ARG B:367 , TYR B:375	BINDING SITE FOR RESIDUE GOL B 407
15	BC6	SOFTWARE	TRP B:173 , CYS B:294 , GLY B:344 , ALA B:348 , BME B:402 , HOH B:698	BINDING SITE FOR RESIDUE EDO B 408

(no "SS Bond" information available for 4JY3)

Asymmetric Unit

No.	Residues
1	Trp A:206	-	Pro A:207
2	Val A:238	-	Pro A:239
3	Trp B:206	-	Pro B:207
4	Val B:238	-	Pro B:239

(no "SAP(SNP)/Variant" information available for 4JY3)

(no "PROSITE Motif" information available for 4JY3)

(no "Exon" information available for 4JY3)

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
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Chain A from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh..eeeee...........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhh..eee....eeeee...eeee....eee..eeee.....hhhhhhhh..eeeee...eeeeeeee..hhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhhh.....ee..eeeee...ee..eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jy3 A  10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379

Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh..eeeee...........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhh..eee....eeeee...eeee....eee..eeee.....hhhhhhhh..eeeee...eeeeeeee..hhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhh......ee..eeeee...ee..eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jy3 B  10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379

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 4JY3)

(no "CATH Domain" information available for 4JY3)

(no "Pfam Domain" information available for 4JY3)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Trp A:206 - Pro A:207	[ RasMol ]
		Trp B:206 - Pro B:207	[ RasMol ]
		Val A:238 - Pro A:239	[ RasMol ]
		Val B:238 - Pro B:239	[ RasMol ]

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	4jy3
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4jy2	UNLIGANDED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (4, 4)

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