2A7P - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE G81A MUTANT OF THE ACTIVE CHIMERA OF (S)-MANDELATE DEHYDROGENASE IN COMPLEX WITH ITS SUBSTRATE 3-INDOLELACTATE

Authors :   N. Sukumar, Y. Xu, B. Mitra, F. S. Mathews

Date :   05 Jul 05 (Deposition) - 11 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Tim Barrel, Hydroxy Acid Oxidizing Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sukumar, A. Dewanti, A. Merli, G. L. Rossi, B. Mitra, F. S. Mathews
Structures Of The G81A Mutant Form Of The Active Chimera Of (S)-Mandelate Dehydrogenase And Its Complex With Two Of Its Substrates.
Acta Crystallogr. , Sect. D V. 65 543 2009
PubMed-ID: 19465768 | Reference-DOI: 10.1107/S0907444909010270
(for further references see the PDB file header)

Molecule 1 - (S)-MANDELATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	3IL	1	Ligand/Ion	3-(INDOL-3-YL) LACTATE
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	3IL	4	Ligand/Ion	3-(INDOL-3-YL) LACTATE
2	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:26 , LEU A:27 , PRO A:79 , THR A:80 , ALA A:81 , SER A:108 , GLN A:129 , TYR A:131 , THR A:156 , LYS A:231 , SER A:253 , HIS A:255 , GLY A:256 , ARG A:258 , ASP A:284 , SER A:285 , GLY A:286 , ARG A:288 , GLY A:307 , ARG A:308 , 3IL A:410 , HOH A:895 , HOH A:896 , HOH A:902 , HOH A:937	BINDING SITE FOR RESIDUE FMN A 390
2	AC2	SOFTWARE	TRP A:87 , LYS A:89 , ASP A:240 , ILE A:243 , LYS A:276 , THR A:277	BINDING SITE FOR RESIDUE MES A 890
3	AC3	SOFTWARE	ALA A:110 , TYR A:131 , ARG A:165 , HIS A:255 , FMN A:390 , HOH A:966 , HOH A:980 , HOH A:981 , HOH A:995	BINDING SITE FOR RESIDUE 3IL A 410

(no "SS Bond" information available for 2A7P)

(no "Cis Peptide Bond" information available for 2A7P)

(no "SAP(SNP)/Variant" information available for 2A7P)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FMN_HYDROXY_ACID_DH_1	PS00557	FMN-dependent alpha-hydroxy acid dehydrogenases active site.	MDLB_PSEPU	272-278	1	A:253-259

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FMN_HYDROXY_ACID_DH_1	PS00557	FMN-dependent alpha-hydroxy acid dehydrogenases active site.	MDLB_PSEPU	272-278	4	A:253-259

(no "Exon" information available for 2A7P)

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:353
 aligned with MDLB_PSEPU | P20932 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:372
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  
           MDLB_PSEPU     4 NLFNVEDYRKLRQKRLPKMVYDYLEGGAEDEYGVKHNRDVFQQWRFKPKRLVDVSRRSLQAEVLGKRQSMPLLIGPTGLNGALWPKGDLALARAATKAGIPFVLSTASNMSIEDLARQCDGDLWFQLYVIHREIAQGMVLKALHTGYTTLVLTTDVAVNGYRERDLHNRFKIPMSYSAKVVLDGCLHPRWSLDFVRHGMPQLANFVSSQTSSLEMQAALMSRQMDASFNWEALRWLRDLWPHKLLVKGLLSAEDADRCIAEGADGVILSNHGGRQLDCAISPMEVLAQSVAKTGKPVLIDSGFRRGSDIVKALALGAEAVLLGRATLYGLAARGETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDYLQNE 375
               SCOP domains d2a7pa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2a7pA00 A:4-356 Aldolase class I                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eee......hhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeeee........hhhhhhhh..........-------------...........------...hhhhhhhh........hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FMN_HYD------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a7p A   4 NLFNVEDYRKLAQKRLPKMVYDYLEGGAEDEYGVKHNRDVFQQWRFKPKRLVDVSRRSLQAEVLGKRQSMPLLIGPTALNGALWPKGDLALARAATKAGIPFVLSTASNMSIEDLARQCDGDLWFQLYVIHREIAQGMVLKALHTGYTTLVLTTDVAVNGYRERDLHNRFKIPPFLTLK-------------NFEGIDLGKMD------KANLEMQAALMSRQMDASFNWEALRWLRDLWPHKLLVKGLLSAEDADRCIAEGADGVILSNHGGRQLDCAISPMEVLAQSVAKTGKPVLIDSGFRRGSDIVKALALGAEAVLLGRATLYGLAARGETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDYLQNE 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        |-         -  |    190  |    194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  
                                                                                                                                                                                                            182           183       193    194

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: automated matches (40)

Pseudomonas putida [TaxId: 303] (4)

d2a7pa_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Pseudomonas putida. Organism_taxid: 303. (7)

2a7pA00

A:4-356

(no "Pfam Domain" information available for 2A7P)

Asymmetric Unit(hide GO term definitions)

Chain A (MDLB_PSEPU | P20932)

molecular function
	GO:0033720	(S)-mandelate dehydrogenase activity	Catalysis of the reaction: (S)-2-hydroxy-2-phenylacetate + acceptor = 2-oxo-2-phenylacetate + reduced acceptor.
	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: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:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0019596	mandelate catabolic process	The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
	GO:0018924	mandelate metabolic process	The chemical reactions and pathways involving mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
	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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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Biological Unit
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1huv	NATIVE CHIMERA OF SAME PROTEIN SOLVED AT 2.15A RESOLUTION
1p4c	NATIVE CHIMERA OF SAME PROTEIN AT OXIDIZED STATE, SOLVED AT 1.35A RESOLUTION
1p5b	NATIVE CHIMERA OF SAME PROTEIN AT REDUCED STATE SOLVED AT 1.35A RESOLUTION
2a7n
2a85

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