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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ACYL-COA DEHYDROGENASE 11
 
Authors :  J. R. C. Muniz, K. Guo, P. Savitsky, A. Roos, W. Yue, E. Pilka, F. Von Delf A. M. Edwards, C. Bountra, C. H. Arrowsmith, J. Weigelt, U. Oppermann
Date :  28 Feb 09  (Deposition) - 12 May 09  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Human, Acyl-Coa, Dehydrogenase, Phosphoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. C. Muniz, K. Guo, P. Savitsky, A. Roos, W. Yue, E. Pilka, F. Von Delft, A. M. Edwards, C. Bountra, C. H. Arrowsmith, J. Weigelt, U. Oppermann
Crystal Structure Of Human Acyl-Coa Dehydrogenase 11
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 469008
    Fragment: RESIDUES 355-780
    Organ: LIVER
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACYL-COA DEHYDROGENASE 11, ACAD-11

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO42Ligand/IonPHOSPHATE ION
3UNX14Ligand/IonUNKNOWN ATOM
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO44Ligand/IonPHOSPHATE ION
3UNX28Ligand/IonUNKNOWN ATOM

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:152 , MET A:154 , THR A:155 , ALA A:160 , SER A:161 , SER A:162 , TRP A:186 , SER A:188 , HIS A:246 , VAL A:397 , LEU A:400 , PRO A:404 , GLU A:406 , VAL A:407 , ARG B:305 , PHE B:308 , LEU B:312 , HIS B:315 , GLU B:316 , GLN B:375 , VAL B:376 , GLY B:378 , GLY B:379BINDING SITE FOR RESIDUE FAD A 600
02AC2SOFTWAREARG A:305 , PHE A:308 , LEU A:312 , HIS A:315 , GLU A:316 , GLN A:375 , VAL A:376 , GLY A:378 , GLY A:379 , PHE B:152 , MET B:154 , THR B:155 , ALA B:160 , SER B:161 , SER B:162 , TRP B:186 , SER B:188 , HIS B:246 , VAL B:397 , LEU B:400 , PRO B:404 , GLU B:406 , VAL B:407BINDING SITE FOR RESIDUE FAD B 600
03AC3SOFTWARELYS A:310 , HIS A:315 , GLU A:316BINDING SITE FOR RESIDUE PO4 A1427
04AC4SOFTWARELYS B:310 , ALA B:314 , HIS B:315 , GLU B:316BINDING SITE FOR RESIDUE PO4 B1426
05AC5SOFTWAREARG A:275 , HIS A:283 , ASP A:402BINDING SITE FOR RESIDUE UNX A1428
06AC6SOFTWARESER A:188BINDING SITE FOR RESIDUE UNX A1429
07AC7SOFTWAREUNX A:1431BINDING SITE FOR RESIDUE UNX A1430
08AC8SOFTWAREUNX A:1430 , UNX A:1432BINDING SITE FOR RESIDUE UNX A1431
09AC9SOFTWAREASN A:390 , UNX A:1431BINDING SITE FOR RESIDUE UNX A1432
10BC1SOFTWAREARG B:275 , ASP B:402 , UNX B:1428BINDING SITE FOR RESIDUE UNX B1427
11BC2SOFTWAREUNX B:1427BINDING SITE FOR RESIDUE UNX B1428
12BC3SOFTWAREASP B:240 , UNX B:1430BINDING SITE FOR RESIDUE UNX B1429
13BC4SOFTWAREASN B:390 , UNX B:1429 , UNX B:1431BINDING SITE FOR RESIDUE UNX B1430
14BC5SOFTWAREASN B:390 , UNX B:1430 , UNX B:1432BINDING SITE FOR RESIDUE UNX B1431
15BC6SOFTWAREUNX B:1431BINDING SITE FOR RESIDUE UNX B1432
16BC7SOFTWAREUNX B:1435BINDING SITE FOR RESIDUE UNX B1434
17BC8SOFTWAREUNX B:1434BINDING SITE FOR RESIDUE UNX B1435

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ala A:118 -Pro A:119
2Gly A:244 -Gly A:245
3Ala B:118 -Pro B:119
4Thr B:207 -Ser B:208
5Gly B:244 -Gly B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WBI)

(-) Sequences/Alignments

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:394
 aligned with ACD11_HUMAN | Q709F0 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:404
                                   383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773    
          ACD11_HUMAN   374 VQTRKGQEVLIKVKHFMKQHILPAEKEVTEFYVQNENSVDKWGKPLVIDKLKEMAKVEGLWNLFLPAVSGLSHVDYALIAEETGKCFFAPDVFNCQAPDTGNMEVLHLYGSEEQKKQWLEPLLQGNITSCFCMTEPDVASSDATNIECSIQRDEDSYVINGKKWWSSGAGNPKCKIAIVLGRTQNTSLSRHKQHSMILVPMNTPGVKIIRPLSVFGYTDNFHGGHFEIHFNQVRVPATNLILGEGRGFEISQGRLGPGRIHHCMRTVGLAERALQIMCERATQRIAFKKKLYAHEVVAHWIAESRIAIEKIRLLTLKAAHSMDTLGSAGAKKEIAMIKVAAPRAVSKIVDWAIQVCGGAGVSQDYPLANMYAITRVLRLADGPDEVHLSAIATMELRDQAKRLT 777
               SCOP domains d2wbia1 A:22-265 automated mat          ches                                                                                                                                                                                                        d2wbia2 A:266-425 automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------2wbiA02 A:150-266 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh----------....hhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhh..eeeee..eeeeeeeeeeee......eeeeeeeee......hhhh.eeeeeee.....eeeeee.......hhhhh.eeeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbi A  22 VQTRKGQEVLIKVKHFMKQHILPAEKEVTE----------KWGKPLVIDKLKEMAKVEGLWNLFLPAVSGLSHVDYALIAEETGKCFFAPDVFNCQAPDTGNMEVLHLYGSEEQKKQWLEPLLQGNITSCFCMTEPDVASSDATNIECSIQRDEDSYVINGKKWWSSGAGNPKCKIAIVLGRTQNTSLSRHKQHSMILVPMNTPGVKIIRPLSVFGYTDNFHGGHFEIHFNQVRVPATNLILGEGRGFEISQGRLGPGRIHHCMRTVGLAERALQIMCERATQRIAFKKKLYAHEVVAHWIAESRIAIEKIRLLTLKAAHSMDTLGSAGAKKEIAMIKVAAPRAVSKIVDWAIQVCGGAGVSQDYPLANMYAITRVLRLADGPDEVHLSAIATMELRDQAKRLT 425
                                    31        41        51         -|       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       401       411       421    
                                                        51         62                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:398
 aligned with ACD11_HUMAN | Q709F0 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:403
                                   383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773   
          ACD11_HUMAN   374 VQTRKGQEVLIKVKHFMKQHILPAEKEVTEFYVQNENSVDKWGKPLVIDKLKEMAKVEGLWNLFLPAVSGLSHVDYALIAEETGKCFFAPDVFNCQAPDTGNMEVLHLYGSEEQKKQWLEPLLQGNITSCFCMTEPDVASSDATNIECSIQRDEDSYVINGKKWWSSGAGNPKCKIAIVLGRTQNTSLSRHKQHSMILVPMNTPGVKIIRPLSVFGYTDNFHGGHFEIHFNQVRVPATNLILGEGRGFEISQGRLGPGRIHHCMRTVGLAERALQIMCERATQRIAFKKKLYAHEVVAHWIAESRIAIEKIRLLTLKAAHSMDTLGSAGAKKEIAMIKVAAPRAVSKIVDWAIQVCGGAGVSQDYPLANMYAITRVLRLADGPDEVHLSAIATMELRDQAKRL 776
               SCOP domains d2wbib1 B:22-265 automated matches                                                                                                                                                                                                                  d2wbib2 B:266-424 automated matches                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------2wbiB02 B:150-266 Butyryl-CoA Dehydrogenase, subunit A, dom     ain 2                                                -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Acyl-CoA_dh_N-2wbiB05 B:24-147                                                                                              ---Acyl-CoA_dh_M-2wbiB03 B:151-206                         -----------------------------------------------------------Acyl-CoA_dh_1-2wbiB01 B:266-417                                                                                                                         ------- Pfam domains (1)
           Pfam domains (2) --Acyl-CoA_dh_N-2wbiB06 B:24-147                                                                                              ---Acyl-CoA_dh_M-2wbiB04 B:151-206                         -----------------------------------------------------------Acyl-CoA_dh_1-2wbiB02 B:266-417                                                                                                                         ------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhh..eeeee..eeeeeeeeeeee......eeeeeeeee.....-----.eeeeeee.....eeeeee.......hhhhh.eeeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbi B  22 VQTRKGQEVLIKVKHFMKQHILPAEKEVTEFYVQNENSVDKWGKPLVIDKLKEMAKVEGLWNLFLPAVSGLSHVDYALIAEETGKCFFAPDVFNCQAPDTGNMEVLHLYGSEEQKKQWLEPLLQGNITSCFCMTEPDVASSDATNIECSIQRDEDSYVINGKKWWSSGAGNPKCKIAIVLGRTQNTS-----QHSMILVPMNTPGVKIIRPLSVFGYTDNFHGGHFEIHFNQVRVPATNLILGEGRGFEISQGRLGPGRIHHCMRTVGLAERALQIMCERATQRIAFKKKLYAHEVVAHWIAESRIAIEKIRLLTLKAAHSMDTLGSAGAKKEIAMIKVAAPRAVSKIVDWAIQVCGGAGVSQDYPLANMYAITRVLRLADGPDEVHLSAIATMELRDQAKRL 424
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      |  -  |    221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421   
                                                                                                                                                                                                                    208   214
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: Acyl-CoA_dh (32)
(-)
Clan: no clan defined [family: Acyl-CoA_dh_M] (24)
(-)
Clan: no clan defined [family: Acyl-CoA_dh_N] (23)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACD11_HUMAN | Q709F0)
molecular function
    GO:0003995    acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0000062    fatty-acyl-CoA binding    Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
    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:0004466    long-chain-acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + ETF = 2,3-dehydroacyl-CoA + reduced ETF.
    GO:0070991    medium-chain-acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a medium-chain fatty acid residue. A medium chain fatty acid is any fatty acid with a chain length of between C6 and C12.
    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.
    GO:0052890    oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a flavin.
    GO:0017099    very-long-chain-acyl-CoA dehydrogenase activity    Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a very long chain fatty acid residue. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22.
biological process
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0033539    fatty acid beta-oxidation using acyl-CoA dehydrogenase    A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    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.
cellular component
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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