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Title :   X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE

Authors :   M. Tegoni, C. Cambillau

Date :   13 Apr 95 (Deposition) - 10 Jul 95 (Release) - 27 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

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

Reference :   M. Tegoni, S. Begotti, C. Cambillau
X-Ray Structure Of Two Complexes Of The Y143F Flavocytochrome B2 Mutant Crystallized In The Presence Of Lactate Or Phenyl Lactate.
Biochemistry V. 34 9840 1995
PubMed-ID: 7632684 | Reference-DOI: 10.1021/BI00031A004

Molecule 1 - L-LACTATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PGR
	Expression System Plasmid	:	PGR 401
	Expression System Taxid	:	562
	Gene	:	PGR
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PYR	2	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PYR	4	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:144 , SER A:195 , ALA A:196 , THR A:197 , ALA A:198 , SER A:228 , GLN A:252 , THR A:280 , LYS A:349 , SER A:371 , HIS A:373 , GLY A:374 , ARG A:376 , ASP A:409 , GLY A:410 , GLY A:411 , ARG A:413 , GLY A:432 , ARG A:433 , PYR A:580 , HOH A:608 , HOH A:612	BINDING SITE FOR RESIDUE FMN A 570
2	AC2	SOFTWARE	LEU A:36 , PHE A:39 , HIS A:43 , PRO A:44 , VAL A:49 , PHE A:62 , HIS A:66 , VAL A:70 , ILE A:71 , ILE A:75 , TYR A:97 , GLN A:139 , LEU A:199 , LEU A:230 , LYS A:296 , PYR A:580	BINDING SITE FOR RESIDUE HEM A 560
3	AC3	SOFTWARE	PHE A:143 , TYR A:254 , ARG A:289 , HIS A:373 , ARG A:376 , HEM A:560 , FMN A:570	BINDING SITE FOR RESIDUE PYR A 580
4	AC4	SOFTWARE	PHE B:143 , TYR B:144 , SER B:195 , ALA B:196 , THR B:197 , ALA B:198 , SER B:228 , GLN B:252 , TYR B:254 , THR B:280 , LYS B:349 , HIS B:373 , GLY B:374 , ARG B:376 , ASP B:409 , GLY B:410 , GLY B:411 , ARG B:413 , GLY B:432 , ARG B:433 , LEU B:436 , PYR B:580	BINDING SITE FOR RESIDUE FMN B 570
5	AC5	SOFTWARE	PHE B:143 , ALA B:198 , TYR B:254 , ARG B:289 , HIS B:373 , ARG B:376 , FMN B:570	BINDING SITE FOR RESIDUE PYR B 580

(no "SS Bond" information available for 1LDC)

(no "Cis Peptide Bond" information available for 1LDC)

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

Asymmetric Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB2_YEAST	119-126	1	A:39-46
2	FMN_HYDROXY_ACID_DH_2	PS51349	FMN-dependent alpha-hydroxy acid dehydrogenase domain profile.	CYB2_YEAST	197-563	2	A:117-483 B:117-483
3	FMN_HYDROXY_ACID_DH_1	PS00557	FMN-dependent alpha-hydroxy acid dehydrogenases active site.	CYB2_YEAST	451-457	2	A:371-377 B:371-377

Biological Unit 1 (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB2_YEAST	119-126	2	A:39-46
2	FMN_HYDROXY_ACID_DH_2	PS51349	FMN-dependent alpha-hydroxy acid dehydrogenase domain profile.	CYB2_YEAST	197-563	4	A:117-483 B:117-483
3	FMN_HYDROXY_ACID_DH_1	PS00557	FMN-dependent alpha-hydroxy acid dehydrogenases active site.	CYB2_YEAST	451-457	4	A:371-377 B:371-377

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML054C	1	YML054C.1	XIII:167308-165533	1776	CYB2_YEAST	1-591	591	2	A:10-511 (gaps) B:102-511 (gaps)	502 410

Asymmetric Unit

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	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:478
 aligned with CYB2_YEAST | P00175 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:502
                                    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       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589  
           CYB2_YEAST    90 KISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLKFSNTKAGPKAMKKTNVEESQGASRALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA 591
               SCOP domains d1ldca2 A:10-97 Flavocytochrome b2, N-terminal domain                                   d1ldca1 A:98-511 Flavocytochrome b2, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ldcA01 A:10-104 Flavocytochrome B2, subunit A, domain 1                                       -------1ldcA02 A:112-493 Aldolase class I                                                                                                                                                                                                                                                                                                                                                            ------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh........eeee..eeee.hhhhhh.....hhhhhh.....hhhhhhh..hhhhhhh..hhh..........hhh..........hhh.hhhhh.......hhh...hhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh............................eee.....hhhh....hhhhhhhhh........eeee......hhhhhh........eeeee.....hhhhhhhhhhhhh....eeeee.........hhhhhh.------------------------...........hhhhhhhhhh...eeeeeee..hhhhhhhhh....eeee.............hhhhhhhhhhhhhh...hhh.eeeee.....hhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh..hhh................hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------CYTOCHRO----------------------------------------------------------------------FMN_HYDROXY_ACID_DH_2  PDB: A:117-483 UniProt: 197-563                                                                                                                                                                                                                                                                                                                         ---------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FMN_HYD-------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:10-511 (gaps) UniProt: 1-591 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 1ldc A  10 KISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAFYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLK------------------------ALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA 511
                                    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      |  -         -         - |     329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509  
                                                                                                                                                                                                                                                                                                                        296                      321

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with CYB2_YEAST | P00175 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:410
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591
           CYB2_YEAST   182 TKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLKFSNTKAGPKAMKKTNVEESQGASRALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA 591
               SCOP domains d1ldcb_ B: Flavocytochrome b2, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ldcB00 B:102-511 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ------------------------------FMN_dh-1ldcB01 B:132-480                                                                                                                                                                                                                                                                                                                                     ------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------FMN_dh-1ldcB02 B:132-480                                                                                                                                                                                                                                                                                                                                     ------------------------------- Pfam domains (2)
           Pfam domains (3) Cyt-b5-1ldcB03 B:102-162                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) Cyt-b5-1ldcB04 B:102-162                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhh......hhh...hhhhhhhhh....hhhhhhhh......hhhhhhhhhhhh.................eee..eee...eee.....hhh.....hhhhhhhhhh.......eeee......hhhhhhh.......eeeee.....hhhhhhhhhhhhhh...eeeee.........hhhhhh.----------------------------.......hhhhhhhhh....eeeeeee..hhhhhhhhh....eeee.............hhhhhhhhhhhhhh..hhhh.eeee......hhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh..hhh................hhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------FMN_HYDROXY_ACID_DH_2  PDB: B:117-483 UniProt: 197-563                                                                                                                                                                                                                                                                                                                         ---------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FMN_HYD-------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:102-511 (gaps) UniProt: 1-591 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 1ldc B 102 TKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAFYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLK----------------------------FIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA 511
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    |    -         -         -   |   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                                                                                                                            296                          325

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Baker's yeast (Saccharomyces cerevisiae) (49)

1a	1ldcA02	A:112-493
1b	1ldcB00	B:102-511

Architecture: Roll (3276)

Topology: Flavocytochrome B2; Chain A, domain 1 (56)

Homologous Superfamily: Flavocytochrome B2, subunit A, domain 1 (56)

Baker's yeast (Saccharomyces cerevisiae) (6)

1ldcA01

A:10-104

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYB2_YEAST | P00175)

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:0004460	L-lactate dehydrogenase (cytochrome) activity	Catalysis of the reaction: (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c.
	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:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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.
biological process
	GO:0006089	lactate metabolic process	The chemical reactions and pathways involving lactate, the anion of lactic acid.
	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:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	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:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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