1HUV - JenaLib

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Title :   CRYSTAL STRUCTURE OF A SOLUBLE MUTANT OF THE MEMBRANE-ASSOCIATED (S)-MANDELATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA AT 2.15A RESOLUTION

Authors :   F. S. Mathews, N. Sukumar

Date :   04 Jan 01 (Deposition) - 19 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

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

Reference :   N. Sukumar, Y. Xu, D. L. Gatti, B. Mitra, F. S. Mathews
Structure Of An Active Soluble Mutant Of The Membrane-Associated (S)-Mandelate Dehydrogenase.
Biochemistry V. 40 9870 2001
PubMed-ID: 11502180 | Reference-DOI: 10.1021/BI010938K

Molecule 1 - L(+)-MANDELATE DEHYDROGENASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Other Details	:	20 RESIDUE INSERTION FROM GLYCOLATE OXIDASE AT RESIDUE 177
	Synonym	:	S-MANDELATE DEHYDROGENASE, MDH

		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	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:131 , ARG A:165 , HIS A:255 , ARG A:258 , FMN A:390 , HOH A:1012 , HOH A:1020	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	TYR A:26 , LEU A:27 , PRO A:79 , THR A:80 , GLY 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 , SO4 A:400 , HOH A:898 , HOH A:925 , HOH A:932 , HOH A:938	BINDING SITE FOR RESIDUE FMN A 390
3	AC3	SOFTWARE	TRP A:87 , LYS A:89 , ASP A:240 , ILE A:243 , LYS A:276 , THR A:277 , HOH A:1019	BINDING SITE FOR RESIDUE MES A 890

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

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

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

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 1HUV)

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:349
 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 d1huva_ A: Membrane-associated (S)-mandelate dehydrogenase                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1huvA00 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........hhhhhhh.........hhh-hh.-------.......---------------hhhhhhh........hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FMN_HYD------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1huv A   4 NLFNVEDYRKLAQKRLPKMVYDYLEGGAEDEYGVKHNRDVFQQWRFKPKRLVDVSRRSLQAEVLGKRQSMPLLIGPTGLNGALWPKGDLALARAATKAGIPFVLSTASNMSIEDLARQCDGDLWFQLYVIHREIAQGMVLKALHTGYTTLVLTTDVAVNGYRERDLHNRFKIPPFLTLKN-FEG-------IDLGKMD---------------EMQAALMSRQMDASFNWEALRWLRDLWPHKLLVKGLLSAEDADRCIAEGADGVILSNHGGRQLDCAISPMEVLAQSVAKTGKPVLIDSGFRRGSDIVKALALGAEAVLLGRATLYGLAARGETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDYLQNE 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 | |     - |     | -         -   |   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  
                                                                                                                                                                                                             183 | |     187   193             198                                                                                                                                                              
                                                                                                                                                                                                               184 |                                                                                                                                                                                            
                                                                                                                                                                                                                 186

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: Membrane-associated (S)-mandelate dehydrogenase (3)

Pseudomonas putida [TaxId: 303] (3)

d1huva_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

1huvA00

A:4-356

(no "Pfam Domain" information available for 1HUV)

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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