2NLI - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN L-LACTATE OXIDASE AND A SUBSTRATE ANALOGUE AT 1.59 ANGSTROM RESOLUTION

Authors :   M. Furuichi, N. Suzuki, D. Balasundaresan, Y. Yoshida, H. Minagawa, Y. H. Kaneko, I. Waga, P. K. R. Kumar, H. Mizuno

Date :   20 Oct 06 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.59

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

Keywords :   L-Lactate Oxidase, Flavoenzyme, Fmn, D-Lactate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Furuichi, N. Suzuki, B. Dhakshnamoorhty, H. Minagawa, R. Yamagishi, Y. Watanabe, Y. Goto, H. Kaneko, Y. Yoshida, H. Yagi, I. Waga, P. K. R. Kumar, H. Mizuno
X-Ray Structures Of Aerococcus Viridans Lactate Oxidase And Its Complex With D-Lactate At Ph 4. 5 Show An Alpha-Hydroxyacid Oxidation Mechanism
J. Mol. Biol. V. 378 436 2008
PubMed-ID: 18367206 | Reference-DOI: 10.1016/J.JMB.2008.02.062

Molecule 1 - LACTATE OXIDASE
	Chains	:	A, B
	EC Number	:	1.13.12.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AEROCOCCUS VIRIDANS
	Organism Taxid	:	1377

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	LAC	2	Ligand/Ion	LACTIC ACID
3	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	FMN	8	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	LAC	8	Ligand/Ion	LACTIC ACID
3	PEO	8	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	LAC	4	Ligand/Ion	LACTIC ACID
3	PEO	4	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 3 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	LAC	4	Ligand/Ion	LACTIC ACID
3	PEO	4	Ligand/Ion	HYDROGEN PEROXIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:92 , PRO A:93 , ILE A:94 , ALA A:95 , SER A:122 , GLN A:144 , TYR A:146 , THR A:172 , LYS A:241 , SER A:263 , HIS A:265 , GLY A:266 , ARG A:268 , ASP A:296 , SER A:297 , GLY A:298 , VAL A:299 , ARG A:300 , GLY A:319 , ARG A:320 , LAC A:1376 , PEO A:1377 , HOH A:1379 , HOH A:1395 , HOH A:1408	BINDING SITE FOR RESIDUE FMN A 1375
2	AC2	SOFTWARE	TYR A:40 , ALA A:95 , TYR A:124 , TYR A:146 , THR A:176 , ARG A:268 , FMN A:1375 , PEO A:1377	BINDING SITE FOR RESIDUE LAC A 1376
3	AC3	SOFTWARE	HIS A:265 , FMN A:1375 , LAC A:1376	BINDING SITE FOR RESIDUE PEO A 1377
4	AC4	SOFTWARE	ILE B:41 , ALA B:92 , PRO B:93 , ILE B:94 , ALA B:95 , SER B:122 , GLN B:144 , TYR B:146 , THR B:172 , LYS B:241 , SER B:263 , HIS B:265 , GLY B:266 , ARG B:268 , ASP B:296 , SER B:297 , GLY B:298 , VAL B:299 , ARG B:300 , GLY B:319 , ARG B:320 , LAC B:2376 , PEO B:2377 , HOH B:2379 , HOH B:2385 , HOH B:2394	BINDING SITE FOR RESIDUE FMN B 2375
5	AC5	SOFTWARE	TYR B:40 , ALA B:95 , TYR B:146 , ARG B:268 , FMN B:2375 , PEO B:2377	BINDING SITE FOR RESIDUE LAC B 2376
6	AC6	SOFTWARE	HIS B:265 , FMN B:2375 , LAC B:2376	BINDING SITE FOR RESIDUE PEO B 2377

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

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

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

(no "PROSITE Motif" information available for 2NLI)

(no "Exon" information available for 2NLI)

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:352
 aligned with Q44467_9LACT | Q44467 from UniProtKB/TrEMBL  Length:374

    Alignment length:368
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
         Q44467_9LACT     7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
               SCOP domains d2nlia_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eee......hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....eeee....---...--------....hhhhhhhhh.hhhhh-----........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee............hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nli A   7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADST---NRD--------YPFGMPIVQRYLRGTAEGM-----YGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   | |   -    |  196       206  |    216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
                                                                                                                                                                                                   176 180 |      191               209   215                                                                                                                                                               
                                                                                                                                                                                                         182

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with Q44467_9LACT | Q44467 from UniProtKB/TrEMBL  Length:374

    Alignment length:368
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
         Q44467_9LACT     7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVKNKFVYPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
               SCOP domains d2nlib_ B: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------FMN_dh-2nliB01 B:29-367                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (1)
           Pfam domains (2) ----------------------FMN_dh-2nliB02 B:29-367                                                                                                                                                                                                                                                                                                                            ------- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eee......hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....eeee...------------------------------------------.....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeee............hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nli B   7 EYNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADS------------------------------------------SKQKISPRDIEEIAGHSGLPVFVKGIQHPEDADMAIKRGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166        |-         -         -         -         - |     226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
                                                                                                                                                                                                  175                                        218

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: automated matches (48)

Protein domain: automated matches (48)

Aerococcus viridans [TaxId: 1377] (5)

1a	d2nlia_	A:
1b	d2nlib_	B:

(no "CATH Domain" information available for 2NLI)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: FMN_dh (23)

Aerococcus viridans (2)

1a	FMN_dh-2nliB01	B:29-367
1b	FMN_dh-2nliB02	B:29-367

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q44467_9LACT | Q44467)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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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	2nli
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	Q44467_9LACT \| Q44467	:	2du2 2e77 2j6x 2zfa 4rje 4yl2 5ebu

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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

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