Protein sectors: evolutionary units of three-dimensional structure.


Abstract

Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term "protein sectors." Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories.

Submission Details

ID: k2fFYxka

Submitter: Connie Wang

Submission Date: Oct. 22, 2018, 12:21 p.m.

Version: 1

Publication Details
Halabi N;Rivoire O;Leibler S;Ranganathan R,Cell (2009) Protein sectors: evolutionary units of three-dimensional structure. PMID:19703402
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
3FP8 2009-02-17 1.46 Anionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI) determined to the 1.46 A resolution limit
3FP7 2009-02-17 1.46 Anionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI) cleaved at the scissile bond (LYS15-ALA16) determined to the 1.46 A resolution limit
3FP6 2009-02-17 1.49 Anionic trypsin in complex with bovine pancreatic trypsin inhibitor (BPTI) determined to the 1.49 A resolution limit
1F7Z 2001-07-04 1.55 RAT TRYPSINOGEN K15A COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
1DPO 1997-07-07 1.59 STRUCTURE OF RAT TRYPSIN
1J16 2002-12-23 1.6 BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
1F5R 2001-07-04 1.65 RAT TRYPSINOGEN MUTANT COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
1YLC 2006-04-25 1.7 Trypsin/BPTI complex mutant
3TGK 2001-07-04 1.7 TRYPSINOGEN MUTANT D194N AND DELETION OF ILE 16-VAL 17 COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI)
1YLD 2006-04-25 1.7 Trypsin/BPTI complex mutant
1FY8 2000-11-08 1.7 CRYSTAL STRUCTURE OF THE DELTAILE16VAL17 RAT ANIONIC TRYPSINOGEN-BPTI COMPLEX
1YKT 2006-04-25 1.7 Trypsin/Bpti complex mutant
1SLU 1996-07-11 1.8 RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN
3TGI 1998-12-23 1.8 WILD-TYPE RAT ANIONIC TRYPSIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI)
1J15 2002-12-23 2.0 BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
1SLW 1996-07-11 2.0 RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; NICKEL-BOUND
1J17 2002-12-23 2.0 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT
1BRB 1994-07-31 2.1 CRYSTAL STRUCTURES OF RAT ANIONIC TRYPSIN COMPLEXED WITH THE PROTEIN INHIBITORS APPI AND BPTI
1SLX 1996-07-11 2.2 RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; ZINC-BOUND
1ANE 1997-04-01 2.2 ANIONIC TRYPSIN WILD TYPE
1ANC 1997-04-01 2.2 ANIONIC TRYPSIN MUTANT WITH SER 214 REPLACED BY LYS
1BRA 1994-04-30 2.2 RELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN
3TGJ 1998-12-23 2.2 S195A TRYPSINOGEN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI)
1K9O 2001-11-21 2.3 CRYSTAL STRUCTURE OF MICHAELIS SERPIN-TRYPSIN COMPLEX
1QL9 2000-08-25 2.3 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT
1SLV 1996-07-11 2.3 RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; COPPER-BOUND
1EZS 2000-06-23 2.3 CRYSTAL STRUCTURE OF ECOTIN MUTANT M84R, W67A, G68A, Y69A, D70A BOUND TO RAT ANIONIC TRYPSIN II
1AND 1997-04-01 2.3 ANIONIC TRYPSIN MUTANT WITH ARG 96 REPLACED BY HIS
1TRM 1988-07-16 2.3 THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE OF ASP102 IN SERINE PROTEASE CATALYSIS
1EZU 2000-06-23 2.4 ECOTIN Y69F, D70P BOUND TO D102N TRYPSIN
1J14 2002-12-23 2.4 BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT
1AMH 1997-12-24 2.5 UNCOMPLEXED RAT TRYPSIN MUTANT WITH ASP 189 REPLACED WITH SER (D189S)
1BRC 1994-05-31 2.5 RELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN
2TRM 1988-07-16 2.8 THE THREE-DIMENSIONAL STRUCTURE OF ASN102 MUTANT OF TRYPSIN. ROLE OF ASP102 IN SERINE PROTEASE CATALYSIS
1ANB 1997-04-01 2.8 ANIONIC TRYPSIN MUTANT WITH SER 214 REPLACED BY GLU

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Anionic trypsin-2 P00763 TRY2_RAT