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(-) Description

Title :  HYDROGENOBACTER THERMOPHILUS CYTOCHROME C552 DIMER FORMED BY DOMAIN SWAPPING AT N-TERMINAL REGION
 
Authors :  C. Ren, S. Nagao, M. Yamanaka, H. Kamikubo, H. Komori, Y. Shomura, Y. Hig S. Hirota
Date :  08 Jun 15  (Deposition) - 21 Oct 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.26
Chains :  Asym. Unit :  A,C,E,G
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  E,G  (1x)
Keywords :  Electron Transfer, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ren, S. Nagao, M. Yamanaka, H. Komori, Y. Shomura, Y. Higuchi, S. Hirota
Oligomerization Enhancement And Two Domain Swapping Mode Detection For Thermostable Cytochrome C552Via The Elongatio Of The Major Hinge Loop.
Mol Biosyst V. 11 3218 2015
PubMed-ID: 26451671  |  Reference-DOI: 10.1039/C5MB00545K

(-) Compounds

Molecule 1 - CYTOCHROME C-552
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JCB387
    Expression System Taxid: 562
    Gene: HTH_0988, HYDTH_0984
    Organism Scientific: HYDROGENOBACTER THERMOPHILUS (STRAIN DSM 6534 / IAM 12695 / TK-6)
    Organism Taxid: 608538
    Strain: DSM 6534 / IAM 12695 / TK-6
    Synonym: CYTOCHROME C552

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACEG
Biological Unit 1 (1x): AC  
Biological Unit 2 (1x):   EG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1HEC4Ligand/IonHEME C
2IOD11Ligand/IonIODIDE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
2IOD10Ligand/IonIODIDE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
2IOD1Ligand/IonIODIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:69 , HOH A:273binding site for residue IOD A 102
02AC2SOFTWAREGLN A:7 , HOH A:257 , HOH A:268 , GLN G:7binding site for residue IOD A 103
03AC3SOFTWARELYS A:50 , LYS A:51binding site for residue IOD A 104
04AC4SOFTWAREHOH A:254 , HOH A:277binding site for residue IOD A 105
05AC5SOFTWAREGLN A:65binding site for residue IOD A 108
06AC6SOFTWARECYS A:10 , CYS A:13 , HIS A:14 , PRO C:26 , TYR C:28 , TYR C:35 , TYR C:44 , LYS C:48 , ILE C:49 , GLY C:53 , SER C:54 , GLY C:55 , VAL C:56 , TRP C:57 , GLY C:58 , VAL C:60 , MET C:62 , GLN C:65 , HOH C:210 , HOH C:213binding site for residue HEC C 101
07AC7SOFTWAREGLN C:7 , HOH C:262 , HOH C:271 , GLN E:7binding site for residue IOD C 103
08AC8SOFTWAREARG E:38binding site for residue IOD E 102
09AC9SOFTWAREALA A:5 , LYS A:8 , GLY A:9 , MET A:11 , ALA A:12 , CYS A:13 , HIS A:14 , PRO A:26 , TYR A:28 , TYR A:35 , TYR A:44 , LYS A:48 , ILE A:49 , SER A:54 , GLY A:55 , VAL A:56 , TRP A:57 , GLY A:58 , VAL A:60 , MET A:62 , GLN A:65 , HOH A:208 , HOH A:227 , ALA C:5 , LYS C:8 , GLY C:9 , MET C:11 , ALA C:12 , CYS C:13 , HIS C:14 , PRO C:26 , TYR C:28 , TYR C:35 , TYR C:44 , LYS C:48 , ILE C:49 , GLY C:53 , SER C:54 , GLY C:55 , VAL C:56 , TRP C:57 , GLY C:58 , VAL C:60 , MET C:62 , GLN C:65 , HOH C:210 , HOH C:213 , SER G:59binding site for Di-peptide HEC A 101 and CYS C 10
10AD1SOFTWARESER C:59 , ALA E:5 , LYS E:8 , GLY E:9 , MET E:11 , ALA E:12 , CYS E:13 , HIS E:14 , PRO E:26 , TYR E:28 , TYR E:35 , TYR E:44 , LYS E:48 , ILE E:49 , SER E:54 , GLY E:55 , VAL E:56 , TRP E:57 , GLY E:58 , VAL E:60 , MET E:62 , GLN E:65 , HOH E:204 , HOH E:210 , ALA G:5 , LYS G:8 , GLY G:9 , MET G:11 , ALA G:12 , CYS G:13 , HIS G:14 , PRO G:26 , TYR G:28 , TYR G:35 , TYR G:44 , LYS G:48 , GLY G:53 , SER G:54 , GLY G:55 , VAL G:56 , TRP G:57 , GLY G:58 , VAL G:60 , MET G:62 , HOH G:206 , HOH G:216 , HOH G:224binding site for Di-peptide HEC E 101 and CYS G 10
11AD2SOFTWARESER C:59 , ALA E:5 , LYS E:8 , GLY E:9 , MET E:11 , ALA E:12 , CYS E:13 , HIS E:14 , PRO E:26 , TYR E:28 , TYR E:35 , TYR E:44 , LYS E:48 , ILE E:49 , SER E:54 , GLY E:55 , VAL E:56 , TRP E:57 , GLY E:58 , VAL E:60 , MET E:62 , GLN E:65 , HOH E:204 , HOH E:210 , ALA G:5 , LYS G:8 , GLY G:9 , MET G:11 , ALA G:12 , CYS G:13 , HIS G:14 , PRO G:26 , TYR G:28 , TYR G:35 , TYR G:44 , LYS G:48 , GLY G:53 , SER G:54 , GLY G:55 , VAL G:56 , TRP G:57 , GLY G:58 , VAL G:60 , MET G:62 , HOH G:206 , HOH G:216 , HOH G:224binding site for Di-peptide HEC G 101 and CYS E 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AUR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AUR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AUR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AUR)

(-) Exons   (0, 0)

(no "Exon" information available for 5AUR)

(-) 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:83
                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  5aur A  1 NEQLAKQKGCMACHDLKAGGGKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 83
                                    10        20        30        40        50        60        70        80   


Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  5aur C  1 NEQLAKQKGCMACHDLKAGGGKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 83
                                    10        20        30        40        50        60        70        80   


Chain E from PDB  Type:PROTEIN  Length:83
                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  5aur E  1 NEQLAKQKGCMACHDLKAGGGKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 83
                                    10        20        30        40        50        60        70        80   


Chain G from PDB  Type:PROTEIN  Length:83
                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  5aur G  1 NEQLAKQKGCMACHDLKAGGGKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 83
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AUR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AUR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AUR)

(-) Gene Ontology  (5, 5)

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 Related Entries

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        CY552_HYDTT | P15452: 1ayg 1ynr 2ai5 3vym 4zid 5aus

(-) Related Entries Specified in the PDB File

3vym WILD-TYPE DIMER
5aus