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A P P E N D I X

P R O T E I N S T R U C T U R E SUnd er s t and i ng o f t he mo l ec u l a r me chan i s ms t ha t unde r p i n b i oene r ge t ic s con t i nues t oadvance a s mor e 3 - D s t ruc t u r es o f p r o t e i n s a r e de t e r mi ned . Som e o f t he se s t r uc t u r e s a r ei l l u s t r a t ed i n t h i s book ( e s pec i a l l y i n P l a t e s A t o K) bu t many mor e a r e now ava i l ab l e .Thes e can be acce s s ed on t he P r o t ei n D a t a B a n k ( PDB) h t t p : / / www. r c s b . o r g . Each s t r uc -ture i s g iven a code . A se lec t ion of such codes , toge ther wi th the pro te ins they re fe r to , a reg i ven be l ow f o r p r o t e i n s t ha t a r e r e levan t t o the s ub j ec t ma t t e r o f t h is book . W her e t he p r o -te in i s no t des cr ibed in the tex t , b r ie f de ta i ls o f in te res t ing fea tures a re no ted .

A ve r y va l uab l e com pi l a t i on o f p r o t e i n s t r uc t u r e / f unc t i on i n f o r ma t i on f o r m any o f theme t a l l op r o t e i n s d i s cus s ed i n t h i s book can be f ound i n H a n d b o o k o f M e t a l l o p ro t e in s ,Vol umes 1 and 2 , ed i ted by A . Me s s e r s chm i d t , R . Hube r , T . Pou l o s an d K . Wi egha r d t andpub l i s hed by J . Wi l ey i n 2001 .

* I nd i ca t e s pe r i p l a s mi c l oca t ion i n bac t e ri aProtein Code Com mentsA. Resp iratory electron transfer proteins." (Ch ap ter 5)Am ine dehydrogenase 1JMX

Azurin 4AZU

Carbon mo noxid e dehydrogenase 1QJ2(aerobic)

*A quinohemoprotein witha novel cross-linked activesite cysteine tryptophylquinoneand three novel thioether crosslinks. From Pseudom onas putida;passes electrons to c-typecytochromes or cupredoxins*Type 1 copper protein

- mainly/3 sheet structureHas active site Mo co-ordinatedby 1M CD (molybdopterin-cytosine dinucleotide) and anS-selenylcysteine. Associated withproteins carrying Fe/S centres an dFAD. Feeds electrons into aCO-insensitive respiratory chain

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::;:;: :~:~ :!~ ,:i, B I O E N E R G E T I C S 3

Protein Code CommentsCytochrome aa3 oxidase

Cytochrome aa3 oxidaseCytochrome ba3 oxidase

1AR1

1OCC1EHK

Cyt0chrome bcl complex 1BCCCytochrome bc l complex 1BE3Cytochrome bcl complex 1BGYCytochrome bcl complex 1E2VCytochrome c 1HRCCytochrome c2 2CXBCytochrome c3 2CYR

Cytochrome c peroxidase 1EB72CYP

Cytochrome c550 1COTD. lactate dehydrogenase 1FOXDMSO (dimethylsulphoxide)reductase

Formate dehydrogenaseFumarate reductase

Two subunits of P ar acoccusdeni tr i f icans enzymeBovine heart enzyme oxidizedA distinctive oxidase fromthe thermophile Ther musther moph i lusChicken heartBovine heartBovine heartYeastMitochondrial from horse heart

Hydrogenase

Hydroxylamine oxidoreductase

*R hodobac ter s phaer o ides*A tetra heme c-typecytochrome found in sulfatereducing bacteria*From P s eudomonas aer ug inos a;is a diheme c-type cytochromeA b-type cytochrome from theinter-membrane space of yeastmitochondria*Paracoccus deni tr i f icansPeripheral membrane proteinfrom E. coli

1CXS1DMR4DMR1DMS1EU11KQF

*Has active site Mo co-ordinatedby two MGD (molybdopterin-guanosine dinucleotide)molecules, each of whichprovides two sulfur ligands;other ligands to Mo varySee Plate E

1FUM1QLA1D4E

2FRV

1FGJ

See Plate E*A flavo c-type cytochromeenzyme from S hewane l lapu tr e fac iens*From Des u l fov ibrio g ig as has aNi-Fe active site. Donateselectrons to cytochrome c3*Trimeric enzyme that catalysesoxidation of hydroxylamine tonitrite. Has eight c-type hemesper polypeptide one of which,with a cross-link to a tyrosine,forms the active site. Found inNi t r os omonas bacteria

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APPENDIX 28 ,5

Pro te in C o d e C o m m e n t sM e t h a n o l d e h y d r o g e n a s e

M e t h y l a m i n e d e h y d r o g e n a s e

M e t h y l - c o e n z y m e M r e d u ct a se

N i t r a te r e duc ta se (pe r ip la smic -N a p)

Nitr i te reduc tase with f ive c - typeh e m e s

N i t r i t e r educ ta se c y toc hrom e cdl

N it r i t e - r e duc ta se Cu- type

N i t rous ox ide r e duc ta se

Pse udoa z ur in

1H4I

2 B B K

1 M R O

2 N A P

1 Q D B

1AOF1 Q K S1N IR1 A F N

1 Q N I1 F W X

3PAZ8PAZ

*Ac t ive s i te PQQ wi th in a n e igh tb l a d e d / 3 p r o p e l l e r*Con ta ins two c ros s - l inke d a ndmodi f ie d t ryp toph a ns a t a c t ives i te w i th in a s e ve n b la de d/3 pro pe l le rCon ta ins Ni a t ac t ive s i te aspar t of F430*Conta ins a c t ive s it e Mo bo undb y t w o M G D m o l e c u le s* A m m o n i a i s r ea c t io np r o d u c t . U n u s u a l C X X C K h e m ebind ing mo t i f a t a c tive s i te*Nitr ic oxide is reac t ion produc t ;c - ty p e c y t o c h r o m e d o m a i na c c e p ts e le c t rons f rom c - typec y toc hrome o r c upre dox ins a ndis o~ heli cal; t he spe cializ edac t ive s i te d I hem e is loca tedwi th in a n e igh t b la de d /3 p rope l le rs truc ture . Diffe rences in s t ruc tureb e t w e e n t h e e n z y m e s f r o mPseu d o mo n a s a eru g in o sa an dParacoccus panto trophus; thela t t er unde rg oe s a r e ma rka b lec onforma t iona l c ha nge uponre duc t ionF r o m P. panto trop hus r e duc e dF r o m P. panto trop hus ox id iz e dF r o m P. aeruginos a ox id iz e d*Nitr ic oxide is reac t ion produc t .A tr imer . Three type 1 Cu ionsac t as the e lec tron acceptorsf rom o the r p ro te ins ; th re etype 2 C u ions a re a t the ac t ivesites*C onta in s both CUA s i tese e n in c y toc hrome aa 3 ox ida seplus a nove l ac t ive s i te Cuzwi th 4 Cu b r id ge d by a n S a tom.The ac t ive s i te is enc los ed in as e v e n - b l a d e d / 3 - p r o p e l l e rs truc ture . From P s e u d o m o n a snaut ica an d P. denitri f icans* T y pe 1 c o p p e r p r o t e i n - m a i n l y]3 shee t s t ruc ture . O xidize d andre duc e d fo rms f rom Alca l i gen esfa eca l i s

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286 BIOENERGETICS3

P r o t e in C o d e C o m m e n t sR u s t i c y a n i n 1 A 8 Z

Sulf i te oxidas e 1SOX

T M A O ( T r i m e t h y la m i n e - N - o x i d e ) 1 T M Ore duc ta se

B. Photosynthet ic proteins: (Chapter 6)B a c t e r i o r h o d o p s i nBa c te r ia pho tosyn the t ic r e a c t ion c e n t re

C y t o c h r o m e - fH a l o r h o d o p s i nL H C I IL H 2P h o t o s y s t e m 1P h o t o s y s t e m 2P la s toc ya n in

C. AT P synthase: (Chapter 7)Bovine he a r t F1Bovine he a r t F IBov ine he a r t F lBovine hear t F1 inhibi torE. coli: F1 ~ subunitT hy la k o id F1Yeast F a + c ring

D. Tran sport proteins." (Chapter 8)E. coli glycerol fac i l i ta torE. coli Msb pro te in

1 C 3 W1 P C R2 P R C1 H C Z1 E l 2N ot de pos i te d1 K 2 U1JBO1FE1l A G 67 P C Y

1 B M F1E791H8E1 G M U1 A B V1 K M H1QO1

1FX81JSQ

*T ype 1 Cu p ro te in f romT. ferrooxida nsChicken l iver f rom inte r-mitochondria l space . Act ive s i teMo c o-ord ina te d by a p te r in* F r o m Shew anel la m assil ia;has ac t ive s i te Mo co-ordina tedb y t w o M G D g r o up s

F r o m R. sphaeroidesF r o m R. viridisUnusu a l c - type c y toc hrom e wi th/3-sheet structureSp ina c hCi rc u la r O ~ 9 / ~ s truc tureR. acidophiliaF r o m S . elongatusF r o m S . elongatusFrom sp ina c h

The o r igina l 2 .8 A s truc ture ofthe F l par tCon ta ins the centra l s ta lk regionor igina l ly not seen (2 .4 A)A form w ith a l l ca ta lyt ic s itesoc c up ie dCoi le d c o i lN - t e r m i n a l d o m a i nHa s inh ib i to r t e n tox in bound3.9 A re solut ion but sho ws r ingof 10 c subunits

A pass ive fac i l i ta t ion of thec y t o p la s m i c m e m b r a n eFirs t s t ruc tura l information a t4 . 5 A re so lu t ion fo r a n AB C- typeAT Pa se. A hom odim e r wi the a c h subun i t p rov id ing s ixtrans-m emb rane ce he l ices and anuc le o t ide -b ind ing doma in . T hehe l ic e s pa c k so a s to p rov ide ac ha mb e r tha t i s e xpose d to thec y top la smic ha l f o f the b i l a ye r