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(-) Description

Title :  OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS
 
Authors :  C. Frazao, D. C. Simes, R. Coelho, D. Alves, M. K. Williamson, P. A. Price, M. L. Cancela, M. A. Carrondo
Date :  21 May 04  (Deposition) - 10 Sep 04  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Calcium-Binding Protein, Osteocalcin, Bone Gla Protein, Bgp, Hydroxyapatite, Gamma Carboxyl Glutamic Acid, Vitamin K, Bone, Mineralization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Frazao, D. C. Simes, R. Coelho, D. Alves, M. K. Williamson, P. A. Price, M. L. Cancela, M. A. Carrondo
Structural Evidence Of A Fourth Gla Residue In Fish Osteocalcin: Biological Implications
Biochemistry V. 44 1234 2005
PubMed-ID: 15667217  |  Reference-DOI: 10.1021/BI048336Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OSTEOCALCIN
    Chains: A, B, C
    Organism Common: MEAGRE
    Organism Scientific: ARGYROSOMUS REGIUS
    Organism Taxid: 172269

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1CGU12Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
2MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CGU4Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CGU4Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CGU4Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECGU A:11 , CGU A:15 , HOH A:2008 , HOH C:2013BINDING SITE FOR RESIDUE MG A1046
2AC2SOFTWARECGU B:11 , CGU B:15 , HOH C:2003 , HOH C:2019BINDING SITE FOR RESIDUE MG B1045
3AC3SOFTWARECGU B:18 , ASP B:24 , MG B:1047 , HOH B:2017 , HOH B:2035 , HOH B:2037 , CGU C:25BINDING SITE FOR RESIDUE MG B1046
4AC4SOFTWARECGU B:18 , ASP B:24 , MG B:1046 , HOH B:2022 , CGU C:25 , HOH C:2064BINDING SITE FOR RESIDUE MG B1047
5AC5SOFTWARECGU B:25 , CGU C:18 , ASP C:24 , MG C:1047 , HOH C:2067 , HOH C:2068BINDING SITE FOR RESIDUE MG C1046
6AC6SOFTWARECGU B:25 , CGU C:18 , ASP C:24 , MG C:1046 , HOH C:2044 , HOH C:2066 , HOH C:2074BINDING SITE FOR RESIDUE MG C1047
7AC7SOFTWAREHOH A:2021 , HOH A:2031 , CGU C:11 , CGU C:15BINDING SITE FOR RESIDUE MG C1048
8AC8SOFTWARECGU C:18 , HOH C:2009 , HOH C:2020 , HOH C:2021 , HOH C:2022 , HOH C:2036BINDING SITE FOR RESIDUE MG C1049

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:17 -A:23
2B:17 -B:23

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VZM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.OSTCN_ARGRE61-93
 
 		  3A:9-41
B:9-41
C:9-41
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.OSTCN_ARGRE63-88
 
 		  3A:11-36
B:11-36
C:11-36
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.OSTCN_ARGRE61-93
 
 		  1A:9-41
-
-
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.OSTCN_ARGRE63-88
 
 		  1A:11-36
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.OSTCN_ARGRE61-93
 
 		  1-
B:9-41
-
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.OSTCN_ARGRE63-88
 
 		  1-
B:11-36
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLA_2PS50998 Gla domain profile.OSTCN_ARGRE61-93
 
 		  1-
-
C:9-41
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.OSTCN_ARGRE63-88
 
 		  1-
-
C:11-36

(-) Exons   (0, 0)

(no "Exon" information available for 1VZM)

(-) 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:43
 aligned with OSTCN_ARGRE | Q800Y1 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:43
                                    64        74        84        94   
           OSTCN_ARGRE   55 KELTLAQTESLREVCETNMACDEMADAQGIVAAYQAFYGPIPF 97
               SCOP domains d1vzma_ A: automated matches                SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------GLA_2  PDB: A:9-41 UniProt: 61-93---- PROSITE (1)
                PROSITE (2) --------GLA_1  PDB: A:11-36       --------- PROSITE (2)
                 Transcript ------------------------------------------- Transcript
                  1vzm A  3 KELTLAQTeSLReVCeTNMACDeMADAQGIVAAYQAFYGPIPF 45
                                    12  |  |  22  |     32        42   
                                   11-CGU  |     25-CGU                
                                       15-CGU                          
                                          18-CGU                       


Chain B from PDB  Type:PROTEIN  Length:42
 aligned with OSTCN_ARGRE | Q800Y1 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:42
                                    65        75        85        95  
           OSTCN_ARGRE   56 ELTLAQTESLREVCETNMACDEMADAQGIVAAYQAFYGPIPF 97
               SCOP domains d1vzmb_ B: automated matches               SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----GLA_2  PDB: B:9-41 UniProt: 61-93---- PROSITE (1)
                PROSITE (2) -------GLA_1  PDB: B:11-36       --------- PROSITE (2)
                 Transcript ------------------------------------------ Transcript
                  1vzm B  4 ELTLAQTeSLReVCeTNMACDeMADAQGIVAAYQAFYGPIPF 45
                                   |13 |  |   23 |      33        43  
                                  11-CGU  |     25-CGU                
                                      15-CGU                          
                                         18-CGU                       


Chain C from PDB  Type:PROTEIN  Length:41
 aligned with OSTCN_ARGRE | Q800Y1 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:41
                                    66        76        86        96 
           OSTCN_ARGRE   57 LTLAQTESLREVCETNMACDEMADAQGIVAAYQAFYGPIPF 97
               SCOP domains d1vzmc_ C: automated matches              SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                PROSITE (1) ----GLA_2  PDB: C:9-41 UniProt: 61-93---- PROSITE (1)
                PROSITE (2) ------GLA_1  PDB: C:11-36       --------- PROSITE (2)
                 Transcript ----------------------------------------- Transcript
                  1vzm C  5 LTLAQTeSLReVCeTNMACDeMADAQGIVAAYQAFYGPIPF 45
                                  | 14|  |    24|       34        44 
                                 11-CGU  |     25-CGU                
                                     15-CGU                          
                                        18-CGU
   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, 3)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VZM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VZM)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (OSTCN_ARGRE | Q800Y1)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0031214    biomineral tissue development    Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation.
    GO:0030282    bone mineralization    The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
    GO:0030500    regulation of bone mineralization    Any process that modulates the frequency, rate or extent of bone mineralization.
cellular component
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1vzm
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