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Title :   CRYSTAL STRUCTURE OF ACYL-COA DEHYDROGENASE FROM GEOBACILLUS KAUSTOPHILUS

Authors :   L. Chen, L-Q. Chen, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, M Y. Li, Z-Q. Fu, J. P. Rose, B-C. Wang, Southeast Collaboratory For S Genomics (Secsg), Riken Structural Genomics/Proteomics Initi (Rsgi)

Date :   06 Apr 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Gk1316, Acyl-Coa Dehydrogenase, Geobacillus Kaustophilus Hta426, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Chen, L-Q. Chen, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, M. Zhao, Y. Li, Z-Q. Fu, J. P. Rose, B-C. Wang
Crystal Structure Of Acyl-Coa Dehydrogenase From G. Kaustophilus
To Be Published
PubMed: search

Molecule 1 - ACYL-COA DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GK1316
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS
	Organism Taxid	:	235909
	Strain	:	HTA426

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:127 , MET A:129 , THR A:130 , GLY A:135 , SER A:136 , PHE A:160 , ILE A:161 , THR A:162 , GLN A:285 , VAL A:364 , ILE A:367 , TYR A:368 , THR A:371 , GLU A:373 , HOH A:403 , HOH A:409 , HOH A:444 , HOH A:494 , HOH A:542 , ARG B:274 , PHE B:277 , VAL B:281 , PHE B:284 , THR B:286 , GLN B:342 , LEU B:343 , GLY B:346 , HOH B:454 , HOH B:462	BINDING SITE FOR RESIDUE FAD A 401
2	AC2	SOFTWARE	ARG A:274 , PHE A:277 , VAL A:281 , PHE A:284 , THR A:286 , GLN A:342 , LEU A:343 , GLY A:346 , HOH A:424 , HOH A:503 , ILE B:127 , MET B:129 , THR B:130 , GLY B:135 , SER B:136 , PHE B:160 , ILE B:161 , THR B:162 , GLN B:285 , VAL B:364 , ILE B:367 , TYR B:368 , THR B:371 , GLU B:373 , MET B:374 , HOH B:406 , HOH B:416 , HOH B:438 , HOH B:497	BINDING SITE FOR RESIDUE FAD B 401

(no "SS Bond" information available for 2PG0)

Asymmetric Unit

No.	Residues
1	Lys A:181	-	Pro A:182
2	Gly B:149	-	Asp B:150
3	Lys B:181	-	Pro B:182

(no "SAP(SNP)/Variant" information available for 2PG0)

(no "PROSITE Motif" information available for 2PG0)

(no "Exon" information available for 2PG0)

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
	(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:380
 aligned with Q5L0D5_GEOKA | Q5L0D5 from UniProtKB/TrEMBL  Length:381

    Alignment length:380
                                    11        21        31        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
         Q5L0D5_GEOKA     2 TARYLREEHHMFRAAFRKFLEKEAYPHYNDWEKRGIIPRSFWAKMGENGFLCPWVDEKYGGLNADFAYSVVINEELEKVGSSLVGIGLHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEPGAGSDLANISTTAVKDGDYYIVNGQKTFITNGIHADLIVVACKTDPQAKPPHRGISLLVVERDTPGFTRGRKLEKVGLHAQDTAELFFQDAKVPAYNLLGEEGKGFYYLMEKLQQERLVVAIAAQTAAEVMFSLTKQYVKQRTAFGKRVSEFQTVQFRLAEMATEIALGRTFVDRVIEEHMAGKQIVTEVSMAKWWITEMAKRVAAEAMQLHGGYGYMEEYEIARRYRDIPVSAIYAGTNEMMKTIIARQLDL 381
               SCOP domains d2pg0a1 A:6-235 automated matches                                                                                                                                                                                                     d2pg0a2 A:236-385 automated matches                                                                                                                    SCOP domains
               CATH domains --2pg0A01 A:8-124 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                       2pg0A02 A:125-233 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                             --2pg0A03 A:236-384 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                     - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhh..eeeee..eeeeeeeeeee.......eeeeeee......hhhh.eeeeeee.....eee..............eeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pg0 A   6 TARYLREEHHMFRAAFRKFLEKEAYPHYNDWEKRGIIPRSFWAKMGENGFLCPWVDEKYGGLNADFAYSVVINEELEKVGSSLVGIGLHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEPGAGSDLANISTTAVKDGDYYIVNGQKTFITNGIHADLIVVACKTDPQAKPPHRGISLLVVERDTPGFTRGRKLEKVGLHAQDTAELFFQDAKVPAYNLLGEEGKGFYYLMEKLQQERLVVAIAAQTAAEVMFSLTKQYVKQRTAFGKRVSEFQTVQFRLAEMATEIALGRTFVDRVIEEHMAGKQIVTEVSMAKWWITEMAKRVAAEAMQLHGGYGYMEEYEIARRYRDIPVSAIYAGTNEMMKTIIARQLDL 385
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385

Chain B from PDB  Type:PROTEIN  Length:377
 aligned with Q5L0D5_GEOKA | Q5L0D5 from UniProtKB/TrEMBL  Length:381

    Alignment length:377
                                    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       
         Q5L0D5_GEOKA     4 RYLREEHHMFRAAFRKFLEKEAYPHYNDWEKRGIIPRSFWAKMGENGFLCPWVDEKYGGLNADFAYSVVINEELEKVGSSLVGIGLHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEPGAGSDLANISTTAVKDGDYYIVNGQKTFITNGIHADLIVVACKTDPQAKPPHRGISLLVVERDTPGFTRGRKLEKVGLHAQDTAELFFQDAKVPAYNLLGEEGKGFYYLMEKLQQERLVVAIAAQTAAEVMFSLTKQYVKQRTAFGKRVSEFQTVQFRLAEMATEIALGRTFVDRVIEEHMAGKQIVTEVSMAKWWITEMAKRVAAEAMQLHGGYGYMEEYEIARRYRDIPVSAIYAGTNEMMKTIIARQLD 380
               SCOP domains d2pg0b1 B:8-235 automated matches                                                                                                                                                                                                   d2pg0b2 B:236-384 automated matches                                                                                                                   SCOP domains
               CATH domains 2pg0B01 B:8-124 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                       2pg0B02 B:125-233 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                             --2pg0B03 B:236-384 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                                      CATH domains
           Pfam domains (1) ---Acyl-CoA_dh_N-2pg0B05 B:11-122                                                                                  ---Acyl-CoA_dh_M-2pg0B03 B:126-177                     ---------------------------------------------------------Acyl-CoA_dh_1-2pg0B01 B:235-383                                                                                                                      - Pfam domains (1)
           Pfam domains (2) ---Acyl-CoA_dh_N-2pg0B06 B:11-122                                                                                  ---Acyl-CoA_dh_M-2pg0B04 B:126-177                     ---------------------------------------------------------Acyl-CoA_dh_1-2pg0B02 B:235-383                                                                                                                      - Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhh..eeeee..eeeeeeeeeee.......eeeeeee......hhhh.eeeeeee.....eee..............eeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pg0 B   8 RYLREEHHMFRAAFRKFLEKEAYPHYNDWEKRGIIPRSFWAKMGENGFLCPWVDEKYGGLNADFAYSVVINEELEKVGSSLVGIGLHNDIVTPYIASYGTEEQKQKWLPKCVTGELITAIAMTEPGAGSDLANISTTAVKDGDYYIVNGQKTFITNGIHADLIVVACKTDPQAKPPHRGISLLVVERDTPGFTRGRKLEKVGLHAQDTAELFFQDAKVPAYNLLGEEGKGFYYLMEKLQQERLVVAIAAQTAAEVMFSLTKQYVKQRTAFGKRVSEFQTVQFRLAEMATEIALGRTFVDRVIEEHMAGKQIVTEVSMAKWWITEMAKRVAAEAMQLHGGYGYMEEYEIARRYRDIPVSAIYAGTNEMMKTIIARQLD 384
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377

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(hide GO term definitions)

Chain A,B (Q5L0D5_GEOKA | Q5L0D5)

molecular function
	GO:0003995	acyl-CoA dehydrogenase activity	Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
	GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

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	Cis Peptide Bonds
		Gly B:149 - Asp B:150	[ RasMol ]
		Lys A:181 - Pro A:182	[ RasMol ]
		Lys B:181 - Pro B:182	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

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