3GMC - JenaLib

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Title :   CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE WITH SUBSTRATE BOUND

Authors :   K. M. Mcculloch, T. Mukherjee, T. P. Begley, S. E. Ealick

Date :   13 Mar 09 (Deposition) - 14 Apr 09 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Flavin Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Mcculloch, T. Mukherjee, T. P. Begley, S. E. Ealick
Structure Of The Plp Degradative Enzyme 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase From Mesorhizobium Loti Maff303099 And Its Mechanistic Implications.
Biochemistry V. 48 4139 2009
PubMed-ID: 19317437 | Reference-DOI: 10.1021/BI900149F
(for further references see the PDB file header)

Molecule 1 - 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	XF1
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MLR6788
	Organism Common	:	MESORHIZOBIUM LOTI
	Organism Scientific	:	MESORHIZOBIUM LOTI
	Organism Taxid	:	381

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	3HM	2	Ligand/Ion	5-HYDROXY-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	3HM	1	Ligand/Ion	5-HYDROXY-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3HM	1	Ligand/Ion	5-HYDROXY-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	3HM	2	Ligand/Ion	5-HYDROXY-6-METHYLPYRIDINE-3-CARBOXYLIC ACID
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	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 , TYR A:270 , GLY A:287 , ASP A:288 , GLY A:300 , ALA A:301 , GLY A:302 , 3HM A:381 , HOH A:384 , HOH A:423 , HOH A:426 , HOH A:482 , HOH A:484 , HOH A:512 , HOH A:601 , HOH A:620 , HOH A:654	BINDING SITE FOR RESIDUE FAD A 380
2	AC2	SOFTWARE	TYR A:54 , ARG A:211 , LEU A:213 , PRO A:295 , ALA A:296 , ALA A:298 , FAD A:380 , HOH A:435 , HOH A:484 , HOH A:493 , HOH A:546 , HOH A:654	BINDING SITE FOR RESIDUE 3HM A 381
3	AC3	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 , TYR B:270 , GLY B:287 , ASP B:288 , GLY B:300 , ALA B:301 , GLY B:302 , 3HM B:381 , HOH B:383 , HOH B:402 , HOH B:462 , HOH B:463 , HOH B:479 , HOH B:502 , HOH B:517 , HOH B:527 , HOH B:657 , HOH B:705	BINDING SITE FOR RESIDUE FAD B 380
4	AC4	SOFTWARE	TYR B:54 , ARG B:211 , LEU B:213 , MET B:227 , PRO B:295 , ALA B:296 , ALA B:298 , LEU B:352 , FAD B:380 , HOH B:463 , HOH B:480 , HOH B:481 , HOH B:517 , HOH B:726	BINDING SITE FOR RESIDUE 3HM B 381

(no "SS Bond" information available for 3GMC)

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 3GMC)

(no "PROSITE Motif" information available for 3GMC)

(no "Exon" information available for 3GMC)

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:369
 aligned with Q988D3_RHILO | Q988D3 from UniProtKB/TrEMBL  Length:379

    Alignment length:369
                                    20        30        40        50        60        70        80        90       100       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         
         Q988D3_RHILO    11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee..........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhh..eeee...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
                 3gmc A  11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    20        30        40        50        60        70        80        90       100       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

Chain B from PDB  Type:PROTEIN  Length:369
 aligned with Q988D3_RHILO | Q988D3 from UniProtKB/TrEMBL  Length:379

    Alignment length:369
                                    20        30        40        50        60        70        80        90       100       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         
         Q988D3_RHILO    11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee..........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhhh.eeee...eeeee...eeee....eee..eeee.....hhhhhhhh..eeeee...eeeeeeee.hhhhhh......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
                 3gmc B  11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    20        30        40        50        60        70        80        90       100       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

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 3GMC)

(no "CATH Domain" information available for 3GMC)

(no "Pfam Domain" information available for 3GMC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q988D3_RHILO | Q988D3)

molecular function
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	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.

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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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3gmb	CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (0, 0)

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