2QYT - JenaLib

Title :   CRYSTAL STRUCTURE OF 2-DEHYDROPANTOATE 2-REDUCTASE FROM PORPHYROMONAS GINGIVALIS W83

Authors :   K. Tan, R. Wu, S. Moy, A. Joachimiak, Midwest Center For Structural (Mcsg)

Date :   15 Aug 07 (Deposition) - 04 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Apc81190, 2-Dehydropantoate 2-Reductase, Porphyromonas Gingivalis W83, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, R. Wu, S. Moy, A. Joachimiak
The Crystal Structure Of 2-Dehydropantoate 2-Reductase From Porphyromonas Gingivalis W83.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:15 , LYS A:89 , ALA A:141 , ARG A:142 , LYS A:143 , SO4 A:318 , EDO A:320 , HOH A:443 , HOH A:444	BINDING SITE FOR RESIDUE SO4 A 315
02	AC2	SOFTWARE	LEU A:13 , ALA A:41 , ARG A:42 , HIS A:45 , LYS A:143 , SO4 A:318 , HOH A:365 , HOH A:393	BINDING SITE FOR RESIDUE SO4 A 316
03	AC3	SOFTWARE	ASP A:32 , GLU A:281 , THR A:282 , GLY A:285 , ARG A:289 , TYR A:305	BINDING SITE FOR RESIDUE SO4 A 317
04	AC4	SOFTWARE	GLY A:12 , LEU A:13 , GLY A:14 , CYS A:87 , THR A:88 , ASP A:90 , SO4 A:315 , SO4 A:316 , EDO A:320 , HOH A:443	BINDING SITE FOR RESIDUE SO4 A 318
05	AC5	SOFTWARE	TYR A:186 , ASN A:187 , EDO A:324 , HOH A:459	BINDING SITE FOR RESIDUE SO4 A 319
06	AC6	SOFTWARE	GLY A:12 , GLY A:14 , GLY A:15 , VAL A:16 , GLY A:17 , CYS A:87 , SO4 A:315 , SO4 A:318	BINDING SITE FOR RESIDUE EDO A 320
07	AC7	SOFTWARE	THR A:80 , GLY A:105 , GLN A:106 , THR A:130	BINDING SITE FOR RESIDUE EDO A 321
08	AC8	SOFTWARE	ALA A:293 , ARG A:295 , HOH A:440	BINDING SITE FOR RESIDUE EDO A 322
09	AC9	SOFTWARE	TYR A:19 , ARG A:62 , ASP A:154 , GLU A:156 , ARG A:184 , HOH A:471	BINDING SITE FOR RESIDUE EDO A 323
10	BC1	SOFTWARE	TYR A:186 , ASN A:187 , PRO A:188 , TYR A:194 , SO4 A:319	BINDING SITE FOR RESIDUE EDO A 324

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:287
 aligned with Q7MT04_PORGI | Q7MT04 from UniProtKB/TrEMBL  Length:314

    Alignment length:307
                                    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       
         Q7MT04_PORGI     4 QPIKIAVFGLGGVGGYYGAMLALRAAATDGLLEVSWIARGAHLEAIRAAGGLRVVTPSRDFLARPTCVTDNPAEVGTVDYILFCTKDYDMERGVAEIRPMIGQNTKILPLLNGADIAERMRTYLPDTVVWKGCVYISARKSAPGLITLEADRELFYFGSGLPEQTDDEVRLAELLTAAGIRAYNPTDIDWYIMKKFMMISVTATATAYFDKPIGSILTEHEPELLSLLEEVAELFRAKYGQVPDDVVQQLLDKQRKMPPESTSSMHSDFLQGGSTEVETLTGYVVREAEALRVDLPMYKRMYRELVS 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qytA01 A:4-189 NAD(P)-binding Rossmann-like Domain                                                                                                                                       2qytA02 A:190-310 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; doma                    in 2                           CATH domains
               Pfam domains ----ApbA-2qytA01 A:8-165                                                                                                                                          ------------------------ApbA_C-2qytA02 A:190-310                                                                                                  Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh.eeee....eeee...eee.hhhhhh.eeeeee.....hhhhhhhhhh..eeeeeeeee.....hhhhhhh.........eeeee..eeeee..eeee.....eeeee......hhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh--------------------...hhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qyt A   4 QPIKIAVFGLGGVGGYYGAmLALRAAATDGLLEVSWIARGAHLEAIRAAGGLRVVTPSRDFLARPTCVTDNPAEVGTVDYILFCTKDYDmERGVAEIRPmIGQNTKILPLLNGADIAERmRTYLPDTVVWKGCVYISARKSAPGLITLEADRELFYFGSGLPEQTDDEVRLAELLTAAGIRAYNPTDIDWYImKKFmmISVTATATAYFDKPIGSILTEHEPELLSLLEEVAELFRAKYGQVPDDVVQQLLDKQRKm--------------------ETLTGYVVREAEALRVDLPmYKRmYRELVS 310
                                    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      |  -         -       283       293      |303|      
                                              23-MSE                                                                93-MSE   103-MSE             123-MSE                                                                  196-MSE|                                                        260-MSE              281                300-MSE      
                                                                                                                                                                                                                              200-MSE                                                                                                 304-MSE  
                                                                                                                                                                                                                               201-MSE

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q7MT04_PORGI | Q7MT04)

molecular function
	GO:0008677	2-dehydropantoate 2-reductase activity	Catalysis of the reaction: (R)-pantoate + NADP(+) = 2-dehydropantoate + H(+) + NADPH.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	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.
	GO:0015940	pantothenate biosynthetic process	The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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