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(-) Description

Title :  (M)L214N MUTANT OF THE RHODOBACTER SPHAEROIDES REACTION CENTER
 
Authors :  R. G. Saer, A. Hardjasa, M. E. P. Murphy, J. T. Beatty
Date :  04 Jan 13  (Deposition) - 05 Jun 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  H,L,M
Keywords :  Electron Transfer, Chromatophore, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Saer, A. Hardjasa, F. I. Rosell, A. G. Mauk, M. E. Murphy, J. T. Beatty
Role Of Rhodobacter Sphaeroides Photosynthetic Reaction Center Residue M214 In The Composition, Absorbance Properties, And Conformations Of H(A) And B(A) Cofactors.
Biochemistry V. 52 2206 2013
PubMed-ID: 23480277  |  Reference-DOI: 10.1021/BI400207M

(-) Compounds

Molecule 1 - REACTION CENTER PROTEIN H CHAIN
    Chains: H
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: PUHA
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
    Synonym: PHOTOSYNTHETIC REACTION CENTER H SUBUNIT
 
Molecule 2 - REACTION CENTER PROTEIN L CHAIN
    Chains: L
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: PUFL
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
    Synonym: PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
 
Molecule 3 - REACTION CENTER PROTEIN M CHAIN
    Chains: M
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: PUFM
    Mutation: YES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
    Synonym: PHOTOSYNTHETIC REACTION CENTER M SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (14, 30)

Asymmetric/Biological Unit (14, 30)
No.NameCountTypeFull Name
1BCL4Ligand/IonBACTERIOCHLOROPHYLL A
2BPH2Ligand/IonBACTERIOPHEOPHYTIN A
3CDL1Ligand/IonCARDIOLIPIN
4FE1Ligand/IonFE (III) ION
5GGD1Ligand/IonNONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY]-1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER
6GOL7Ligand/IonGLYCEROL
7HTO2Ligand/IonHEPTANE-1,2,3-TRIOL
8K1Ligand/IonPOTASSIUM ION
9LDA5Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
10MG1Ligand/IonMAGNESIUM ION
11PC11Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
12PO41Ligand/IonPHOSPHATE ION
13SPO1Ligand/IonSPHEROIDENE
14U102Ligand/IonUBIQUINONE-10

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA H:25BINDING SITE FOR RESIDUE GOL H 301
02AC2SOFTWAREGGD H:307BINDING SITE FOR RESIDUE GOL H 302
03AC3SOFTWARETRP H:21 , GOL L:311BINDING SITE FOR RESIDUE GOL H 303
04AC4SOFTWARETHR H:63 , PHE H:64 , GOL H:306 , ALA L:198 , ASN L:199 , PRO L:200BINDING SITE FOR RESIDUE GOL H 304
05AC5SOFTWAREMET H:134 , ALA H:137 , PHE H:140BINDING SITE FOR RESIDUE K H 305
06AC6SOFTWAREGLU H:34 , LYS H:62 , GOL H:304 , ASN L:199 , CDL M:409BINDING SITE FOR RESIDUE GOL H 306
07AC7SOFTWAREGLN H:32 , TYR H:40 , ASN H:52 , GLY H:54 , GOL H:302 , ALA L:1 , PRO L:28 , ARG M:253 , GLY M:257 , U10 M:407BINDING SITE FOR RESIDUE GGD H 307
08AC8SOFTWARETYR L:128 , PHE L:146 , HIS L:153 , BCL L:306 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , GLY M:211 , ASN M:214 , BCL M:402 , LDA M:403 , BPH M:412BINDING SITE FOR RESIDUE BCL L 301
09AC9SOFTWARESER L:178 , U10 L:305BINDING SITE FOR RESIDUE LDA L 304
10BC1SOFTWARETHR L:182 , LEU L:189 , HIS L:190 , LEU L:193 , GLU L:212 , ASP L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LDA L:304 , LEU M:47 , LDA M:404 , PC1 M:410BINDING SITE FOR RESIDUE U10 L 305
11BC2SOFTWAREPHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , LEU L:131 , VAL L:157 , THR L:160 , TYR L:162 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:301 , TYR M:210 , BCL M:401 , BCL M:402 , U10 M:407 , BPH M:412BINDING SITE FOR RESIDUE BCL L 306
12BC3SOFTWAREHIS H:126 , GLU L:72 , TYR L:73 , LYS L:82 , THR M:21BINDING SITE FOR RESIDUE PO4 L 307
13BC4SOFTWAREGLN L:87 , ILE L:91 , TRP L:142BINDING SITE FOR RESIDUE HTO L 308
14BC5SOFTWAREGLY L:77 , ALA L:78 , LEU L:80BINDING SITE FOR RESIDUE GOL L 310
15BC6SOFTWAREGOL H:303 , GLN L:62 , LDA M:403BINDING SITE FOR RESIDUE GOL L 311
16BC7SOFTWAREHIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:306 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:402 , BPH M:406 , SPO M:408BINDING SITE FOR RESIDUE BCL M 401
17BC8SOFTWAREVAL L:157 , TYR L:162 , BCL L:301 , BCL L:306 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:401 , BPH M:406 , PC1 M:410BINDING SITE FOR RESIDUE BCL M 402
18BC9SOFTWARETRP L:151 , BCL L:301 , GOL L:311 , PRO M:200 , LEU M:204BINDING SITE FOR RESIDUE LDA M 403
19CC1SOFTWAREU10 L:305 , SER M:8BINDING SITE FOR RESIDUE LDA M 404
20CC2SOFTWAREHIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266BINDING SITE FOR RESIDUE FE M 405
21CC3SOFTWAREPHE L:181 , LEU L:185 , LEU L:189 , LEU L:219 , VAL M:126 , TRP M:129 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:401 , BCL M:402BINDING SITE FOR RESIDUE BPH M 406
22CC4SOFTWAREGGD H:307 , GLY L:35 , TRP L:100 , BCL L:306 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , ILE M:265BINDING SITE FOR RESIDUE U10 M 407
23CC5SOFTWAREPHE M:67 , ILE M:70 , GLY M:71 , TRP M:75 , PHE M:105 , SER M:119 , MET M:122 , TRP M:157 , GLY M:161 , TRP M:171 , VAL M:175 , HIS M:182 , BCL M:401BINDING SITE FOR RESIDUE SPO M 408
24CC6SOFTWAREALA H:16 , ILE H:22 , PHE H:23 , TYR H:30 , GOL H:306 , ASN L:199 , PRO L:200 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , TRP M:155 , ARG M:267 , TRP M:271BINDING SITE FOR RESIDUE CDL M 409
25CC7SOFTWAREVAL L:220 , U10 L:305 , SER M:30 , GLY M:31 , BCL M:402BINDING SITE FOR RESIDUE PC1 M 410
26CC8SOFTWAREASN M:214 , BPH M:412BINDING SITE FOR RESIDUE MG M 411
27CC9SOFTWAREALA L:42 , ALA L:96 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , SER L:237 , LEU L:238 , VAL L:241 , BCL L:301 , BCL L:306 , TYR M:210 , ALA M:213 , ASN M:214 , TRP M:252 , MG M:411BINDING SITE FOR RESIDUE BPH M 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IN7)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr H:40 -Pro H:41
2Val H:75 -Pro H:76
3Ala H:138 -Gly H:139
4Arg H:248 -Lys H:249
5Gly M:48 -Pro M:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IN7)

(-) Exons   (0, 0)

(no "Exon" information available for 4IN7)

(-) 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 H from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4in7h1 H:11-35          d4in7h2 H:36-250 Photosynthetic reaction centre                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..........................eeeee....eeeee...........eee........eee..hhhhhhhhhhh.................eee.hhh...eeee.......eeee....eeeeeeeeeee....eeeeeeee.....eeeee.hhhee....eee...hhhhh............hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4in7 H  11 DLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS 250
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250


Chain L from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4in7l_ L: L (light) subunit                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4in7 L   1 ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING 281
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 


Chain M from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4in7m_ M: M (medium) subunit                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...........hhhhh........hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4in7 M   1 AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSANLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHG 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IN7)

(-) Gene Ontology  (13, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala H:138 - Gly H:139   [ RasMol ]  
    Arg H:248 - Lys H:249   [ RasMol ]  
    Gly M:48 - Pro M:49   [ RasMol ]  
    Tyr H:40 - Pro H:41   [ RasMol ]  
    Val H:75 - Pro H:76   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RCEH_RHOSH | P0C0Y7: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4lwy 4n7k 4n7l 4rcr 4tqq 4v9g 5lse 5v33
        RCEL_RHOSH | P0C0Y8: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4lwy 4n7k 4n7l 4rcr 4tqq 4v9g 5lse 5v33
        RCEM_RHOSH | P0C0Y9: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4lwy 4n7k 4n7l 4rcr 4tqq 4v9g 5lse 5v33

(-) Related Entries Specified in the PDB File

4in5 RESIDUE MUTATED TO G INSTEAD OF N
4in6 RESIDUE MUTATED TO A INSTEAD OF N