The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins (doi:10.18419/darus-458)
(The modular structure of α/β-hydrolases: similarity of the N- and C-terminal domains to other proteins)

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Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins

doi:10.18419/darus-458

DaRUS

2019-09-30

1

Bauer, Tabea, 2019, "The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins", https://doi.org/10.18419/darus-458, DaRUS, V1, UNF:6:pbQRgDXU4w7vnxyqxzzuRQ== [fileUNF]

The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins

The modular structure of α/β-hydrolases: similarity of the N- and C-terminal domains to other proteins

doi:10.18419/darus-458

Bauer, Tabea (Universität Stuttgart)

PL145/16-1

EXC2075

031B0571A

DaRUS

Pleiss, Jürgen

Buchholz, Patrick C. F.

2019-09-18

https://doi.org/10.18419/darus-458

Medicine, Health and Life Sciences, Lipase Engineering Database, sequence-structure-function relationships

To analyse the structural similarities of the N- and C-terminal domains, representative protein structures of each oxyanion hole type from the proteins of alpha/beta-hydrolase superfamilies 8 to 12 were selected from the Lipase Engineering Database (<a href="https://led.biocatnet.de/">https://led.biocatnet.de/</a>). The structures of the N- and C-terminal domains and the core domains were extracted and saved in separate .pdb files, which were then used to compare the domains by the "all against all" structure comparison tool on the Dali webserver (<a href="http://ekhidna2.biocenter.helsinki.fi/dali/">http://ekhidna2.biocenter.helsinki.fi/dali/</a>). In a second step, the PDB (Protein Data Bank) search tool on the Dali server was used to compare the N- and C-terminal domains against all structures in PDB25, a subset resulting from clustering the whole PDB database with an identity threshold of 25%. The Dali server has different measures to determine similarity between proteins. The Z-Score is a measure for structural similarity, where a Z-score >2 implies significant structural similarities and thus a similar fold. Besides the Z-Score, the output also contains information about the root-mean-square deviation (rmsd) and the sequence identity.

hits from database search

protein structure comparison

root-mean-square deviation

sequence identity

alignment length

Z-score

Abbreviations: DPPIV: human dipeptidyl peptidase IV, APAP: acylaminoacyl peptidase from Aeropyrum pernix K1, RCE: Rhodococcus sp. MB1 cocaine esterase, HPL: human pancreatic lipase, PSML: Pseudomonas sp. MIS38 lipase, HEP: human epoxide hydrolase

Bauer, T. L., Buchholz, P. C. F. and Pleiss, J. (2019), The modular structure of α/β‐hydrolases. FEBS J.

10.1111/febs.15071

Bauer, T. L., Buchholz, P. C. F. and Pleiss, J. (2019), The modular structure of α/β‐hydrolases. FEBS J.

• Number of cases: 173

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:UT/tuDCkMGlPeUykEk1hsw==

• Number of cases: 103

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:ZKUns1L0wMyZIEclSuHQVQ==

• Number of cases: 154

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:bAQkev4V9Lkkkj8oTELKlg==

• Number of cases: 10

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:/rbtvGkBUcWV/wLnakHqRg==

• Number of cases: 35

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:XqW8mARoKShCASUYwLo1pA==

• Number of cases: 41

• No. of variables per record: 9

• Type of File: text/tab-separated-values

UNF:6:bklMJ1HASVPCxiIVaP7wyQ==

• # Job: 2HU5A search # Query: s001A # No: - # Job: 2HU5A search # Query: s001A # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?
• # Job: 1NU8A search # Query: s001A # No: - # Job: 1NU8A search # Query: s001A # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?
• # Job: 6AUM search # Query: s001A # No: - # Job: 6AUM search # Query: s001A # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?
• # Job: 1LPBB search # Query: s001B # No: - # Job: 1LPBB search # Query: s001B # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?
• # Job: 2Z8XA search # Query: s001A # No: - # Job: 2Z8XA search # Query: s001A # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?
• # Job: 1JU4A search # Query: s001A # No: - # Job: 1JU4A search # Query: s001A # No:
• Chain - Chain
• Z - Z
• rmsd - rmsd
• lali - lali
• nres - nres
• id % - id %
• Description - Description
• a/b hydrolase? - a/b hydrolase?

f392 Location:

Variable Format: character

Notes: UNF:6:BSBAlEEl5KHsEvIDsST0tg==

f392 Location:

Variable Format: character

Notes: UNF:6:Dt7QCHJMus6RLUeu57OwmQ==

f392 Location:

Summary Statistics: Mean 14.828323699421967; Max. 50.6; Min. 2.1; StDev 5.028911305428372; Valid 173.0;

Variable Format: numeric

Notes: UNF:6:MXC9PLbyGOkii62rEJP/+w==

f392 Location:

Summary Statistics: Min. 0.4; Max. 15.3; Valid 173.0; StDev 1.7285240532338209; Mean 3.9815028901734104

Variable Format: numeric

Notes: UNF:6:cgw8EuLJY1DasAcs3OVR4A==

f392 Location:

Summary Statistics: Valid 173.0; StDev 39.1803189385002; Min. 54.0; Mean 235.23121387283243; Max. 311.0

Variable Format: numeric

Notes: UNF:6:pA/k+90yjN0GmaQOQR8ZRQ==

f392 Location:

Summary Statistics: Mean 498.94797687861274; Min. 161.0; StDev 214.02853172915755; Max. 1234.0; Valid 173.0;

Variable Format: numeric

Notes: UNF:6:74HoAPHv5pxB6ZpsFLnEPw==

f392 Location:

Summary Statistics: StDev 7.291493846331501; Min. 0.0; Mean 9.947976878612714; Max. 100.0; Valid 173.0;

Variable Format: numeric

Notes: UNF:6:qV2Imf1LOrsywDYfVjI1VA==

f392 Location:

Variable Format: character

Notes: UNF:6:K27NMkXEhXvLs8x8tbJe0Q==

f392 Location:

Variable Format: character

Notes: UNF:6:DurFs/E5svDpcZLqDbHIUg==

f387 Location:

Variable Format: character

Notes: UNF:6:ohOGXeEBDL+2Y0wUntWrLA==

f387 Location:

Variable Format: character

Notes: UNF:6:lq8TrOog/BG4FEAMb9lffw==

f387 Location:

Summary Statistics: Min. 2.2; Valid 103.0; Mean 10.315533980582524; StDev 6.888691461751392; Max. 53.2

Variable Format: numeric

Notes: UNF:6:zoakFIHoFW4RLyRFnbt7RQ==

f387 Location:

Summary Statistics: Valid 103.0; Max. 13.5; Min. 0.5; Mean 4.987378640776699; StDev 1.7947461239248386

Variable Format: numeric

Notes: UNF:6:ffwx91aHIfUj+c/DQbGYPQ==

f387 Location:

Summary Statistics: StDev 57.44785002994467; Mean 226.68932038834956; Max. 457.0; Valid 103.0; Min. 74.0

Variable Format: numeric

Notes: UNF:6:yOWbQMHQKOL41Kwa6NL+Fw==

f387 Location:

Summary Statistics: Mean 506.29126213592235; StDev 197.98586952291402; Min. 277.0; Max. 1234.0; Valid 103.0

Variable Format: numeric

Notes: UNF:6:N8BwYWSX659YBQ8o8SkHVw==

f387 Location:

Summary Statistics: Min. 3.0; Max. 100.0; Mean 11.165048543689316; StDev 11.942753227563687; Valid 103.0

Variable Format: numeric

Notes: UNF:6:Sl5b9CcDx8dJNwtcsRxMow==

f387 Location:

Variable Format: character

Notes: UNF:6:MVVNoPDf7SgRqzMkeR9Jcg==

f387 Location:

Variable Format: character

Notes: UNF:6:fA0M+7iT+q907If3a5d+RQ==

f388 Location:

Variable Format: character

Notes: UNF:6:I2m2IhOlodd1kO/v5B/Oaw==

f388 Location:

Variable Format: character

Notes: UNF:6:5Sl7sjgmkMV9hMxOpjIORg==

f388 Location:

Summary Statistics: Valid 154.0; Max. 37.4; Min. 2.0; StDev 4.907553176148502; Mean 6.052597402597402

Variable Format: numeric

Notes: UNF:6:OhKCZPuwJgCW2O6roBkO5Q==

f388 Location:

Summary Statistics: Valid 154.0; Max. 6.9; Min. 0.3; Mean 3.4220779220779223; StDev 0.6812375084418592

Variable Format: numeric

Notes: UNF:6:tJiSd0vXYycDh2weAjjEpA==

f388 Location:

Summary Statistics: StDev 32.4266895639754; Mean 112.0; Max. 223.0; Valid 154.0; Min. 47.0

Variable Format: numeric

Notes: UNF:6:gGgZkwRHhJflcK2d0lW4Vg==

f388 Location:

Summary Statistics: Valid 154.0; StDev 95.7084405564768; Mean 295.8051948051948; Min. 122.0; Max. 763.0;

Variable Format: numeric

Notes: UNF:6:tTcwBz6BQT/T/nNN/MFiNg==

f388 Location:

Summary Statistics: Mean 12.285714285714292; Min. 3.0; Max. 100.0; Valid 154.0; StDev 8.600588432304274

Variable Format: numeric

Notes: UNF:6:qTaW06qDuRTJR8Be1V7itA==

f388 Location:

Variable Format: character

Notes: UNF:6:G7KupJVqH3zEqjnFip09tg==

f388 Location:

Variable Format: character

Notes: UNF:6:/pUwyQbPDKcEpZ3VyWDpfA==

f389 Location:

Variable Format: character

Notes: UNF:6:jwS0QKSgobNpMD1YELbmyA==

f389 Location:

Variable Format: character

Notes: UNF:6:bVIp2dPsEm3N+qOhkHfauA==

f389 Location:

Summary Statistics: Mean 7.92; Valid 10.0; Min. 2.0; StDev 6.640749623013622; Max. 23.2

Variable Format: numeric

Notes: UNF:6:9Q8z0SJx/N/fJ7u4cPpupg==

f389 Location:

Summary Statistics: Mean 2.59; Max. 3.6; Min. 0.6; Valid 10.0; StDev 0.8875058685251984;

Variable Format: numeric

Notes: UNF:6:5DjdJg6MOtJJ7dv+kn5ztw==

f389 Location:

Summary Statistics: Min. 62.0; Max. 112.0; StDev 16.759740119968715; Mean 85.0; Valid 10.0;

Variable Format: numeric

Notes: UNF:6:0Zi1107mTRLbsbB3FdAP/A==

f389 Location:

Summary Statistics: Max. 1002.0; Valid 10.0; Mean 502.2; StDev 264.19681216009315; Min. 119.0

Variable Format: numeric

Notes: UNF:6:fDVSz5z1mgq8hTJhaQC6yA==

f389 Location:

Summary Statistics: Valid 10.0; Max. 82.0; Min. 4.0; StDev 23.056693412350157; Mean 17.5

Variable Format: numeric

Notes: UNF:6:nOpBKlVTwIVrkYyLVTlcyA==

f389 Location:

Variable Format: character

Notes: UNF:6:6LR1a9p2Kku8S3izImNw+Q==

f389 Location:

Variable Format: character

Notes: UNF:6:w5WXuOiI4SzLGVIrMbEVTg==

f390 Location:

Variable Format: character

Notes: UNF:6:n69FM7KYV3Fk+/JP35HtBw==

f390 Location:

Variable Format: character

Notes: UNF:6:p3hq/t7y2g5NF68CM052zA==

f390 Location:

Summary Statistics: Valid 35.0; Max. 35.9; StDev 6.299813255869061; Mean 6.199999999999999; Min. 2.0

Variable Format: numeric

Notes: UNF:6:AyBQI3K3QWdnZGR4uwCj7Q==

f390 Location:

Summary Statistics: Min. 0.2; Max. 13.7; Mean 6.365714285714286; StDev 3.7476222153396894; Valid 35.0

Variable Format: numeric

Notes: UNF:6:pdJpGkPo55ur8/KazOMK9g==

f390 Location:

Summary Statistics: Min. 77.0; Mean 111.74285714285715; Valid 35.0; StDev 29.06518319139895; Max. 250.0

Variable Format: numeric

Notes: UNF:6:x5HoY86jWZ/WIytZDg813w==

f390 Location:

Summary Statistics: StDev 281.89036250036685; Max. 1793.0; Min. 137.0; Mean 434.0; Valid 35.0;

Variable Format: numeric

Notes: UNF:6:MOaTtkKGFzDDAnty+H0CIg==

f390 Location:

Summary Statistics: Min. 3.0; Max. 100.0; Mean 13.942857142857138; StDev 16.966997129623103; Valid 35.0

Variable Format: numeric

Notes: UNF:6:m/KyefoT6jiCEYGe6HhhkA==

f390 Location:

Variable Format: character

Notes: UNF:6:5xExS0CepepmftSM8hL2WQ==

f390 Location:

Variable Format: character

Notes: UNF:6:tfQR28d4IxUn1dm46zvJXQ==

f391 Location:

Variable Format: character

Notes: UNF:6:2c5dCcYCU+5bjC5V6ymD+A==

f391 Location:

Variable Format: character

Notes: UNF:6:D+qsXzs7KSCAfXbjYPSoYw==

f391 Location:

Summary Statistics: Valid 41.0; Max. 27.3; StDev 4.403212519037081; Mean 5.885365853658537; Min. 2.6;

Variable Format: numeric

Notes: UNF:6:TWHzrGsDFW78bYHip9r0sw==

f391 Location:

Summary Statistics: Min. 1.7; Valid 41.0; Max. 4.5; Mean 3.5439024390243903; StDev 0.5390031449295098

Variable Format: numeric

Notes: UNF:6:bf5euszPHO7m+YT602hjhQ==

f391 Location:

Summary Statistics: Min. 83.0; Mean 113.92682926829268; Valid 41.0; Max. 207.0; StDev 22.349933158627614

Variable Format: numeric

Notes: UNF:6:P4i9Xu7llUlAuOiYKUXv0A==

f391 Location:

Summary Statistics: Min. 108.0; Valid 41.0; StDev 179.0785425176448; Mean 307.9756097560976; Max. 763.0

Variable Format: numeric

Notes: UNF:6:ZUaa3hhqv34geXZRawmS/g==

f391 Location:

Summary Statistics: Max. 37.0; Valid 41.0; Min. 4.0; Mean 9.536585365853657; StDev 5.7710378658245265;

Variable Format: numeric

Notes: UNF:6:TwJI7CK3Z2TkJP5EavwnJw==

f391 Location:

Variable Format: character

Notes: UNF:6:Y99hGjlGT/rKfXiEyp7U2g==

f391 Location:

Variable Format: character

Notes: UNF:6:Zj2/84PDtAufVrjLKHF9cg==

Label:

Supplements01-1.xlsx

Text:

This file contains the data of the Dali analysis with the additional N- and C-terminal module of the indicated proteins. Column A-H show the result from the Dali analysis. All found structures were additionally analyzed by PyMOL to determine whether they belong to the α/β-hydrolase family and the result is indicated by y/n in column I.

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