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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOCHROME CL FROM HYPHOMICROBIUM DENITRIFICANS
 
Authors :  M. Nojiri, D. Hira, K. Yamaguchi, S. Suzuki
Date :  10 Aug 05  (Deposition) - 10 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron Transfer, Cytochrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nojiri, D. Hira, K. Yamaguchi, T. Okajima, K. Tanizawa, S. Suzuki
Crystal Structures Of Cytochrome C(L) And Methanol Dehydrogenase From Hyphomicrobium Denitrificans: Structural And Mechanistic Insights Into Interactions Between The Two Proteins
Biochemistry V. 45 3481 2006
PubMed-ID: 16533029  |  Reference-DOI: 10.1021/BI051877J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME CL
    Chains: A, B
    Organism Scientific: HYPHOMICROBIUM DENITRIFICANS
    Organism Taxid: 53399
    Strain: A3151

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN10Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY B:74 , ASP B:77 , TYR B:79 , HOH B:1225 , HOH B:1313 , HOH B:1432BINDING SITE FOR RESIDUE ZN B 1203
02AC2SOFTWAREGLY A:64 , HIS A:65 , ILE A:66 , GLU A:68BINDING SITE FOR RESIDUE ZN A 1205
03AC3SOFTWAREHIS A:106 , ASP A:109 , HOH A:1424BINDING SITE FOR RESIDUE ZN A 1206
04AC4SOFTWAREGLY B:64 , HIS B:65 , GLU B:68BINDING SITE FOR RESIDUE ZN B 1207
05AC5SOFTWAREASP B:134 , HOH B:1298 , HOH B:1323BINDING SITE FOR RESIDUE ZN B 1211
06AC6SOFTWAREGLY A:74 , ASP A:77 , TYR A:79 , HOH A:1225 , HOH A:1235 , HOH A:1252BINDING SITE FOR RESIDUE ZN A 1214
07AC7SOFTWAREHIS B:106 , ASP B:109 , HOH B:1410BINDING SITE FOR RESIDUE ZN B 1218
08AC8SOFTWAREGLU B:3BINDING SITE FOR RESIDUE ZN B 1219
09AC9SOFTWAREGLU A:153 , HOH A:1309BINDING SITE FOR RESIDUE ZN A 1220
10BC1SOFTWARESER A:58 , CYS A:59 , CYS A:62 , HIS A:63 , PRO A:73 , TRP A:80 , THR A:81 , TYR A:82 , ASN A:85 , LEU A:91 , THR A:94 , ALA A:99 , ASN A:100 , MET A:103 , HIS A:106 , ILE A:122 , HOH A:1225 , HOH A:1266 , HOH A:1305BINDING SITE FOR RESIDUE HEM A 200
11BC2SOFTWARESER B:58 , CYS B:59 , CYS B:62 , HIS B:63 , PRO B:73 , LEU B:75 , TRP B:80 , THR B:81 , TYR B:82 , ASN B:85 , LEU B:91 , ILE B:95 , ALA B:99 , ASN B:100 , MET B:103 , HIS B:106 , ILE B:122 , HOH B:1242 , HOH B:1318 , HOH B:1432BINDING SITE FOR RESIDUE HEM B 201

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:47 -A:165
2B:47 -B:165

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D0W)

(-) Exons   (0, 0)

(no "Exon" information available for 2D0W)

(-) 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:168
 aligned with Q4AE24_9RHIZ | Q4AE24 from UniProtKB/TrEMBL  Length:193

    Alignment length:168
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        
         Q4AE24_9RHIZ    24 AQEVFRNTVTGEALDVEGQAPKEGRDTPAVKQFMQTGVDPYVEVAGCLPKGEEIYLESCSGCHGHIGEGKVGPGLNDSYWTYPKNTTDKGLFETIFGGANGMMGPHGQDLELDNMLKLIAWIRHIQKDDVADADWLSDEQKKNFKPFDIKAWEATGKAAAEKAQCKIS 191
               SCOP domains d2d0wa_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains 2d0wA00 A:1-168 Cytochrome c                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh...........hhhhhhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d0w A   1 AQEVFRNTVTGEALDVEGQAPKEGRDTPAVKQFMQTGVDPYVEVAGCLPKGEEIYLESCSGCHGHIGEGKVGPGLNDSYWTYPKNTTDKGLFETIFGGANGMMGPHGQDLELDNMLKLIAWIRHIQKDDVADADWLSDEQKKNFKPFDIKAWEATGKAAAEKAQCKIS 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with Q4AE24_9RHIZ | Q4AE24 from UniProtKB/TrEMBL  Length:193

    Alignment length:168
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        
         Q4AE24_9RHIZ    24 AQEVFRNTVTGEALDVEGQAPKEGRDTPAVKQFMQTGVDPYVEVAGCLPKGEEIYLESCSGCHGHIGEGKVGPGLNDSYWTYPKNTTDKGLFETIFGGANGMMGPHGQDLELDNMLKLIAWIRHIQKDDVADADWLSDEQKKNFKPFDIKAWEATGKAAAEKAQCKIS 191
               SCOP domains d2d0wb_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains 2d0wB00 B:1-168 Cytochrome c                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh...........hhhhhhh....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d0w B   1 AQEVFRNTVTGEALDVEGQAPKEGRDTPAVKQFMQTGVDPYVEVAGCLPKGEEIYLESCSGCHGHIGEGKVGPGLNDSYWTYPKNTTDKGLFETIFGGANGMMGPHGQDLELDNMLKLIAWIRHIQKDDVADADWLSDEQKKNFKPFDIKAWEATGKAAAEKAQCKIS 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4AE24_9RHIZ | Q4AE24)
molecular function
    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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0015945    methanol metabolic process    The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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2d0v METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS