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Title :   CRYSTAL STRUCTURE OF HUMAN BETA-HYDROXYISOBUTYRYL-COA HYDROLASE IN COMPLEX WITH QUERCETIN

Authors :   E. S. Pilka, C. Phillips, O. N. F. King, K. Guo, F. Von Delft, A. C. W. Pike C. H. Arrowsmith, J. Weigelt, A. M. Edwards, U. Oppermann, Structural Consortium (Sgc)

Date :   19 Dec 07 (Deposition) - 08 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Coenzyme A, Hydrolase, Beta-Hydroxyisobutyryl Acid, Quercetin, Structural Genomics Consortium, Sgc, Branched-Chain Amino Acid Catabolism, Disease Mutation, Mitochondrion, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. S. Pilka, C. Phillips, O. N. F. King, K. Guo, F. Von Delft, A. C. W. Pike, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, U. Oppermann
Crystal Structure Of Human Beta-Hydroxyisobutyryl-Coa Hydrolase In Complex With Quercetin.
To Be Published
PubMed: search

Molecule 1 - 3-HYDROXYISOBUTYRYL-COA HYDROLASE
	Chains	:	A
	EC Number	:	3.1.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-CTHF
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 32-386
	Gene	:	HIBCH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE, HIBYL-COA-H, HIB- COA HYDROLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	HIU	1	Ligand/Ion	(2R)-3-HYDROXY-2-METHYLPROPANOIC ACID
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	QUE	1	Ligand/Ion	3,5,7,3',4'-PENTAHYDROXYFLAVONE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:56 , LEU A:57 , ALA A:59 , GLY A:97 , GLY A:98 , ILE A:100 , PRO A:168 , ILE A:172 , VAL A:349 , LEU A:350 , HIU A:502 , HOH A:886 , HOH A:924	BINDING SITE FOR RESIDUE QUE A 501
2	AC2	SOFTWARE	GLY A:97 , GLY A:98 , ILE A:100 , PHE A:118 , GLU A:121 , GLY A:146 , GLU A:169 , LEU A:174 , ASP A:177 , VAL A:178 , QUE A:501	BINDING SITE FOR RESIDUE HIU A 502

(no "SS Bond" information available for 3BPT)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:360	-	Pro A:361

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031869	T	46	A	HIBCH_HUMAN	Polymorphism	1058180	A	T	46	A
2	UniProt	VAR_031870	Y	122	C	HIBCH_HUMAN	Disease (HIBCHD)	121918329	A	Y	122	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3BPT)

Asymmetric/Biological Unit (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000359678	2a	ENSE00001853401	chr2:191184771-191184442	330	HIBCH_HUMAN	1-12	12	0	-	-
1.3	ENST00000359678	3	ENSE00001419164	chr2:191175522-191175480	43	HIBCH_HUMAN	12-26	15	0	-	-
1.4	ENST00000359678	4	ENSE00001225460	chr2:191161679-191161539	141	HIBCH_HUMAN	27-73	47	1	A:32-73	42
1.5	ENST00000359678	5	ENSE00000964738	chr2:191159356-191159272	85	HIBCH_HUMAN	74-102	29	1	A:74-102	29
1.6	ENST00000359678	6	ENSE00000964739	chr2:191155211-191155131	81	HIBCH_HUMAN	102-129	28	1	A:102-129	28
1.7	ENST00000359678	7	ENSE00002150091	chr2:191152364-191152312	53	HIBCH_HUMAN	129-146	18	1	A:129-146	18
1.10	ENST00000359678	10	ENSE00001794091	chr2:191125960-191125882	79	HIBCH_HUMAN	147-173	27	1	A:147-173	27
1.12c	ENST00000359678	12c	ENSE00001734838	chr2:191117033-191116888	146	HIBCH_HUMAN	173-221	49	1	A:173-221	49
1.15	ENST00000359678	15	ENSE00001709022	chr2:191114452-191114366	87	HIBCH_HUMAN	222-250	29	1	A:222-250	29
1.16b	ENST00000359678	16b	ENSE00001619533	chr2:191110938-191110880	59	HIBCH_HUMAN	251-270	20	1	A:251-270	20
1.18b	ENST00000359678	18b	ENSE00001597377	chr2:191109694-191109613	82	HIBCH_HUMAN	270-297	28	1	A:270-297	28
1.20b	ENST00000359678	20b	ENSE00001692778	chr2:191077801-191077682	120	HIBCH_HUMAN	298-337	40	1	A:298-337	40
1.21a	ENST00000359678	21a	ENSE00002174646	chr2:191073639-191073606	34	HIBCH_HUMAN	338-349	12	1	A:338-349	12
1.22c	ENST00000359678	22c	ENSE00001875591	chr2:191069958-191069360	599	HIBCH_HUMAN	349-386	38	1	A:349-386	38

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:362
 aligned with HIBCH_HUMAN | Q6NVY1 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:362
                                                                                                                                                                                                                                                                                                                                                                                            386       
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    |    -  
          HIBCH_HUMAN    32 TDAAEEVLLEKKGCTGVITLNRPKFLNALTLNMIRQIYPQLKKWEQDPETFLIIIKGAGGKAFCAGGDIRVISEAEKAKQKIAPVFFREEYMLNNAVGSCQKPYVALIHGITMGGGVGLSVHGQFRVATEKCLFAMPETAIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAMLEEDLLALKSPSKENIASVLENYHTESKIDRDKSFILEEHMDKINSCFSANTVEEIIENLQQDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEVLTMEYRLSQACMRGHDFHEGVRAVLIDKDQSPKWKPADLKEVTEEDLNNHFKSLGSSDLKF-------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeeee....eee...hhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeee..eeehhhhhh.....eeee....eee.hhhhh......hhhhhhhhh..hhhhhhhhhh..eehhhhhhh....ee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------A---------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:32-73 UniProt: 27-73     Exon 1.5  PDB: A:74-102      --------------------------Exon 1.7          Exon 1.10  PDB: A:147-173  ------------------------------------------------Exon 1.15  PDB: A:222-250    Exon 1.16b          ---------------------------Exon 1.20b  PDB: A:298-337              Exon 1.21a  -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.6  PDB: A:102-129    -------------------------------------------Exon 1.12c  PDB: A:173-221 UniProt: 173-221      ------------------------------------------------Exon 1.18b  PDB: A:270-297  ---------------------------------------------------Exon 1.22c  PDB: A:349-386            ------- Transcript 1 (2)
                 3bpt A  32 TDAAEEVLLGKKGCTGVITLNRPKFLNALTLNmIRQIYPQLKKWEQDPETFLIIIKGAGGKAFCAGGDIRVISEAEKAKQKIAPVFFREEYmLNNAVGSCQKPYVALIHGITmGGGVGLSVHGQFRVATEKCLFAmPETAIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAmLEEDLLALKSPSKENIASVLENYHTESKIDRDKSFILEEHmDKINSCFSANTVEEIIENLQQDGSSFALEQLKVINKmSPTSLKITLRQLmEGSSKTLQEVLTmEYRLSQACmRGHDFHEGVRAVLIDKDQSPKWKPADLKEVTEEDLNNHFKSLGSSDLKFAENLYFQ 393
                                    41        51        61  |     71        81        91       101       111       121 |     131       141  |    151       161     | 171       181       191       201       211       221  |    231       241       251       261   |   271       281       291       301|      311   |   321      |331     | 341       351       361       371       381       391  
                                                           64-MSE                                                    123-MSE              144-MSE                167-MSE                                                  224-MSE                                  265-MSE                              302-MSE      315-MSE      328-MSE  337-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 '\|'

(no "SCOP Domain" information available for 3BPT)

(no "CATH Domain" information available for 3BPT)

(no "Pfam Domain" information available for 3BPT)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HIBCH_HUMAN | Q6NVY1)

molecular function
	GO:0003860	3-hydroxyisobutyryl-CoA hydrolase activity	Catalysis of the reaction: 3-hydroxy-2-methylpropanoyl-CoA + H2O = CoA + 3-hydroxy-2-methylpropanoate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0009083	branched-chain amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0006574	valine catabolic process	The chemical reactions and pathways resulting in the breakdown of valine, 2-amino-3-methylbutanoic acid.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:360 - Pro A:361	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 12)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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