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(-) Description

Title :  CRYSTAL STRUCTURE OF KAIB FROM SYNECHOCYSTIS SP.
 
Authors :  K. Hitomi, T. Oyama, S. Han, A. S. Arvai, J. A. Tainer, E. D. Getzoff
Date :  06 Jan 05  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Circadian, Clock, Circadian Clock Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hitomi, T. Oyama, S. Han, A. S. Arvai, E. D. Getzoff
Tetrameric Architecture Of The Circadian Clock Protein Kaib. A Novel Interface For Intermolecular Interactions And Its Impact On The Circadian Rhythm.
J. Biol. Chem. V. 280 19127 2005
PubMed-ID: 15716274  |  Reference-DOI: 10.1074/JBC.M411284200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CIRCADIAN CLOCK PROTEIN KAIB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1143

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1BET5Ligand/IonTRIMETHYL GLYCINE
2IMD3Ligand/IonIMIDAZOLE
3MLT8Ligand/IonMALATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:50 , PRO A:51 , GLN A:52 , HOH A:4184BINDING SITE FOR RESIDUE MLT A 6001
02AC2SOFTWAREASN B:1017 , THR B:1018 , PRO B:1019 , GLN D:3034 , GLN D:3037BINDING SITE FOR RESIDUE MLT B 6002
03AC3SOFTWAREVAL B:1014 , GLY B:1016 , ASN B:1017 , SER B:1021 , LEU B:1025 , ASP B:1046 , LYS B:1049 , VAL B:1086BINDING SITE FOR RESIDUE MLT B 6003
04AC4SOFTWARELYS A:26 , GLU B:1035 , ASN D:3017 , THR D:3018 , PRO D:3019BINDING SITE FOR RESIDUE MLT B 6004
05AC5SOFTWAREGLU B:1056 , LEU B:1093 , TYR B:1094 , LYS C:2067 , ILE C:2068 , LEU C:2069 , PRO C:2070 , PRO C:2071 , HOH C:4032BINDING SITE FOR RESIDUE MLT B 6005
06AC6SOFTWARELYS C:2011 , TYR C:2013 , LYS C:2043 , ILE C:2045 , ASN C:2050 , GLN C:2052 , LEU C:2053 , ASP C:2057BINDING SITE FOR RESIDUE MLT C 6006
07AC7SOFTWARELYS C:2043 , VAL C:2044 , ASP C:2046 , ASN C:2050 , HOH C:4051 , HOH C:4147BINDING SITE FOR RESIDUE MLT C 6007
08AC8SOFTWARELYS A:26 , LEU C:2048 , LYS C:2049 , PRO C:2051 , GLN C:2052 , LYS D:3085BINDING SITE FOR RESIDUE MLT D 6008
09AC9SOFTWARETYR B:1008 , BET B:5004 , GLN C:2037 , ARG D:3023BINDING SITE FOR RESIDUE IMD B 7001
10BC1SOFTWARELYS B:1075 , GLY B:1078 , ASP B:1079 , ARG B:1083 , LYS D:3005BINDING SITE FOR RESIDUE IMD B 7002
11BC2SOFTWAREVAL D:3044BINDING SITE FOR RESIDUE IMD D 7003
12BC3SOFTWAREGLU A:35 , GLN A:37 , BET A:5003 , ARG B:1023 , TYR D:3008 , TYR D:3040 , ILE D:3068BINDING SITE FOR RESIDUE BET D 5001
13BC4SOFTWAREGLN B:1034 , GLU B:1035 , THR D:3018 , GLU D:3084BINDING SITE FOR RESIDUE BET B 5002
14BC5SOFTWAREGLN A:34 , HOH A:4053 , ARG B:1023 , LYS B:1026 , MET B:1027 , ASN B:1030 , BET D:5001BINDING SITE FOR RESIDUE BET A 5003
15BC6SOFTWARETYR B:1040 , ILE B:1068 , LEU B:1069 , PRO B:1070 , ARG B:1074 , HOH B:4057 , IMD B:7001 , ARG D:3023 , LYS D:3026BINDING SITE FOR RESIDUE BET B 5004
16BC7SOFTWAREGLU A:84 , ASN C:2020 , GLU C:2084BINDING SITE FOR RESIDUE BET C 5005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WWJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser C:2002 -Pro C:2003

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WWJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WWJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1WWJ)

(-) 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 A from PDB  Type:PROTEIN  Length:99
 aligned with KAIB_SYNY3 | P74645 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          KAIB_SYNY3      1 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIRE   99
               SCOP domains d1wwja_ A: automated matches                                                                        SCOP domains
               CATH domains 1wwjA00 A:1-99 Glutaredoxin                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee...........eeehhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                1wwj A    1 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIRE   99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with KAIB_SYNY3 | P74645 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:91
                                    15        25        35        45        55        65        75        85        95 
          KAIB_SYNY3      6 KTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDE   96
               SCOP domains d1wwjb_ B: automated matches                                                                SCOP domains
               CATH domains 1wwjB00 B:1006-1096 Glutaredoxin                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...........eeeehhhhhh..hhhhhhhhhhhhhh...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                1wwj B 1006 KTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDE 1096
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095 


Chain C from PDB  Type:PROTEIN  Length:98
 aligned with KAIB_SYNY3 | P74645 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          KAIB_SYNY3      1 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIR   98
               SCOP domains d1wwjc_ C: automated matches                                                                       SCOP domains
               CATH domains 1wwjC00 C:2001-2098 Glutaredoxin                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee...hhhhhhhhhhhhhhhh......eeeeeee...........eeehhhhhhh..hhhhhhhhhhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                1wwj C 2001 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIR 2098
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090        


Chain D from PDB  Type:PROTEIN  Length:98
 aligned with KAIB_SYNY3 | P74645 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          KAIB_SYNY3      1 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIR   98
               SCOP domains d1wwjd_ D: automated matches                                                                       SCOP domains
               CATH domains 1wwjD00 D:3001-3098 Glutaredoxin                                                                   CATH domains
           Pfam domains (1) ----------KaiB-1wwjD01 D:3011-3092                                                          ------ Pfam domains (1)
           Pfam domains (2) ----------KaiB-1wwjD02 D:3011-3092                                                          ------ Pfam domains (2)
           Pfam domains (3) ----------KaiB-1wwjD03 D:3011-3092                                                          ------ Pfam domains (3)
           Pfam domains (4) ----------KaiB-1wwjD04 D:3011-3092                                                          ------ Pfam domains (4)
         Sec.struct. author .....eeeeeeeee...hhhhhhhhhhhhhhhhh.....eeeeeee...........eeehhhhhhh..hhhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                1wwj D 3001 MSPFKKTYVLKLYVAGNTPNSVRALKMLKNILEQEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKILPPPVRKIIGDLSDREKVLIGLDLLYDEIR 3098
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KAIB_SYNY3 | P74645)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
biological process
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.

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